You'd start by combining 8 pieces of zombie flesh (or other flesh thing, such as that thing in the nether added by Natura or Biomes o' Plenty) around a redstone dust. This would give you Receptive Flesh.
Receptive Flesh would be the main material for Fleshcraft early-game. You could put 6 Receptive Flesh with three bones in a crafting grid (with the bones forming a horizontal line in the center) to make a chewer. You'd then put a chest on a tank, and surrounded that with receptive flesh, to form a stomach.
The chewer would be placed on top of the stomach, in-game, and the stomach would need to be above an infinite source of water. The chewer would grind down anything biological, such as wood, food, saplings, bones, etc., and that mulch would then go into the stomach to be digested. The stomach would digest it, and use water for that. The mulch would all give the same amount of energy per tick (more on that later), except hardier things (such as wood blocks) would last longer, and thus give more energy overall. The acidity of the stomach could be adjusted; low acidity would digest slower, giving slightly more energy overall but less energy per tick. High acidity would digest quickly, giving more energy per tick, but the mulch would be used faster, and give slightly less energy in total. The higher the acidity, the less water used (which is only relevant if you're piping the water in from somewhere else).
The stomach would produce two waste-products; gas and solid(ish) waste. The gas would just be biogas, usable by any biogas-using machine, and the solid waste could be used later, or burnt as coal. (Which wouldn't give much heat, but, hey, why not.)
The energy would slowly fade away, and a full stomach would not accept more stuff. However, you could attach a bulbous sack to the stomach- 8 Receptive Flesh around a tank- which would store up the energy. This would pull water out of the stomach, and would need some start-up energy & gas to build up pressure, but would then be an inactive balloon. You could then attach another Bulbous Sack to the first one, and chain them.
The energy would be calories, or something similar, at this point. Which makes a sort of sense, to be honest.
Anything attached directly to the stomach, or other similar things in Fleshcraft, would automatically attach itself literally to the block; the flesh of both blocks would merge between them, creating a tube-with-sphincters sort of piping between them. Because it'd look cool.
Now, by combining 8 Receptive Flesh around a block of redstone, you could make a Primal Neurostem. This would then be surrounded by leather for an Leathery Primal Neurostem, which could then be attached to the stomach. This would start Fleshcraft proper.
From here, you can advance down 4 paths; Flesh, Brain, Limb, and Metal (names obviously not super-important).
The Flesh techtree would be all about growth; food, solar power, building blocks, and so on. It would have soylent brown- renamed to Squirming Flesh-, Photosynthesising Flesh (Crafted: 3 leaves on top of 3 Receptive Flesh on top of 3 vines; it's a solar panel), Living Bricks (4 Receptive Flesh in a square, building material that'd look disgusting-and-yet-cool), and tubes. Tubes in Fleshcraft would be different than in most other mods. All Fleshcraft "machines" would need to be connected to the Neurostem, directly or indirectly. You'd combine a vine with a Receptive Flesh to make a tubing path, and it'd be a tool with multiple uses. Instead of placing down tubes, you'd make a trail from A to B (to C to D, etc.) which would, in time, grow. The tubing would need energy, and while it's growing, digestion would produce half as much energy, and not make any solid waste, since part of the mulch is going for growing the tubing.
Combining bonemeal, water, and Receptive Flesh would give you a bucket of Squirming Goo. The only thing this would be for is that you could then spill it on the ground, and it'd create a fleshy surface. If this fleshy surface does not connect, directly or indirectly, to the stomach, it would rot away. Mobs would not spawn on this flesh, and mobs other than the player would be slowed & damaged. If a mob dies on this surface, it will be digested, giving an amount (depending on the mob) of mulch. This would use a small amount of water and energy.
Most "machines" would need to be placed on fleshy ground.
As long as it's connected to the stem, you could make more stomachs, chewers, and sacks. You could make them as you did the first one, with water sources, but that's boring. Instead, you could put four chewers on top of four stomachs on top of four sacks, and you'd get a digestive block. This'd simply have a larger inventory than what was used previously, would digest more at a time, and thus give more energy/tick than the old one. However, this would need water piped-in, and that's the next part.
You could also place 8 sacks together (4x4x2) to create a larger sacks. While a normal sack would contain 4 buckets of stomach acid and store X amount of energy, a large sack could contain 20 buckets and 5x energy. Then you could combine 4 of those in the same pattern to create a huge sack, which'd contain 1000 buckets of stomach acid and 500x energy.
A chewer in a crafting table, on top of a tank, and both surrounded by receptive flesh (with the chewer in the top-middle spot) would make a sucker. This would provide a good amount of water to your system, and would be placed in a pool of water at least 9x9x9. You'd need to attach a tube to it, but it doesn't need to be on fleshy ground. One of these should provide enough water for you for a while, but adding more is never a bad idea (provided their area of operations does not intersect).
Tubes do not need to connect directly; a sucker does not need to be piped directly to anything that needs water. Instead, everything would be indirectly connected, and share resources. You are, after all, making a single living organism. (To reduce strain, items and liquids would not actually travel in the tubes. But we can pretend they are with the right graphics.) Tubes would grow considerably faster on fleshy ground.
For now, that concludes the Flesh part of the tech tree. The feel I was going for was similar to creep from Starcraft; living tissue that feeds the various organs that are scattered around the hive, with anything else living being absorbed into the organism. Except it'd not be purple, but look like ground-up, mashed-up, semi-digested blob of various biological tissue. However, simply having things connect through fleshy ground is meh, and thus tubes. They'd be similar to the esophagus in animals; muscles constricting to squeeze food into its destination. I feel that this would be a nifty thing to make, graphically-wise; rhythmic pulsing that's expressed through appearance other than colour. I could be wrong, since I can't even draw a stick figure, and I can barely make a calculator in Python. :>
Next is either Brain or Limb.
The limb tree would be focused on making entities. 2 receptive flesh in a vertical pattern, with 3 vines on either side, and a flint at the center-top, would make a tentacle. This could be placed anywhere on fleshy ground, and would attack anything but the player who placed it. An iron golem, surrounded by receptive flesh, would make an Infested Iron Golem. Iron Golems on Fleshy Ground would eventually be Infested, as well. These golems would be identical to normal iron golems, except fleshier and self-repairing (while on fleshy ground). The brain tree would introduce ways to command them.
Feeding receptive flesh to a wolf would infest it, as well, and make an Infested Wolf. Same as normal wolves, except they heal faster, can't breed, and will be able to be commanded.
Armour and tools made out of metal (or gems) will, if at less than 50% durability, get infested. They'd automatically repair while the player is on fleshy ground while wearing it.
All fleshy repair would require energy.
Placing three tanks horizontally in a crafting grid, with receptive flesh below them and trap doors above them, will create an infestation chamber. Having one of those in your system will make eaten NPCs become infested instead. Infested Villagers are basically zombies that don't burn, and are friendly. Infested livestock (chickens, sheep, squid, etc.) would be unusable for anything other than combat. The chamber can, eventually, be configured to only infest X mobs, and have a maximum of Y mobs infested at a time.
A very useful block to have would be the grasping tentacle. Simply combine a tentacle with a chest and a piece of receptive flesh, and place it down. It will automatically reach and grab an item within range (5x5x5 or something, better than hopper).
An oculus can also be made; it's an eye. You put a spider eye in the center of a crafting grid, with glass panes (3, vertically) on top, and receptive flesh under and around it. This you'd place down, and, once connected, allows the organism to see around. You could surround your base with.. the plural of "oculus".. which would allow the organism to, for an example, send infested NPCs to attack hostile mobs around the base, or alert you of a player nearby, and such things. CCTV cameras, fleshcraft-style.
Last in the tree is a Burrower. This would need 3 tentacles, 3 chewers, and 3 diamonds. The burrower will dig out a 3x3 area in the direction in which it is pointed, but can only dig 50 blocks away from fleshy ground. However, it can't store items without research in the brain tree. Burrowers require a lot of energy.
The brain tree would be something fancy. It would be about enhancing the capabilities of the organism, but, if the player is not careful, could turn the organism against the player.
First, make a new neurostem, and don't surround it with leather. Instead, 4 receptive flesh blocks (one in each corner) and 4 bonemeal. You'd combine 9 of these stems to create gray matter. Placing 3x3x3 gray matter together in a cube would create the multiblock Brain.
The brain would have a GUI, with multiple tabs. The first tab would be overview; energy made, stored, and used; water stored, gathered, and used; the mass of the organism, its brainpower, its sentience, and its independence.
The second tab would be settings, primarily for multiplayer; you can name your organism, tell it what players it should not attack, what NPCs it should not eat, what it should not infest, and how deep & far burrowers are allowed to burrow. You can also name a player (or a player's organism) as an enemy. This will make the organism wish to attack said player/organism.
The third tab would be a large inventory, where you can enhance its brain. But before I go into that, I'll need to explain brainpower, sentience, and independence. And in this section, I am shamelessly "inspired" by Mike, from The Moon is a Harsh Mistress.
Brainpower is the organisms ability to calculate, measure, and sense. Increasing the brainpower increases the amount of energy gained by [Technobabble goes here]. It also makes readings more accurate (ie, energy in/out, water in/out), and, if sufficient, allows you to tell the organism to allow mob spawns at a point using redstone poker (Redstone torch with flint and receptive flesh), telling not to grow fleshy ground, telling to grow fleshy ground, and so on. It's basically your command-stick. Higher brainpower allows the organism to see with more clarity, and respond more accurately to stimuli; such as, if it sees a creeper, it may surround the creeper with liquid before attacking. Or maybe it'll just push it away. Or drown it.
The redstone poker (or command-stick or whatever it should be called) would be used for all things which in other mods would be used with a wrench or landmarks.
Increasing brainpower increases independence and sentience (because [Technobabble]). Independence is the organisms ability to think for itself, while sentience gives it a sense of self. A sentient, independent organism might decide it doesn't need you, or even that you are a threat, an oppressor, or just food. High independence might make it grow things that it considers it needs, expand the fleshy ground, create more tubing, or ignore orders.
Sentience would be expressed in the fourth tab, communication. There it will tell you what it wants; the organism might want to expand, but if its not independent enough, it won't do so without your permission. It may also want a cooked chicken, or a mushroom soup. Perhaps it wants more infested wolfs. It's also where you tell it what you want; how to handle situations, NPCs, and so on.
Sentience might also make it lie, or play jokes. For an example, it might tell you that it's running out of water, that it has an infinite amount of energy, or it might lift you up with a tentacle, maybe throw you up. Or it may pat you.
Since these features may become annoying, and will become dangerous, the responsible thing to do is to suppress them. You do that with crystal focusers; a diamond surrounded by glass panes will lower the organisms sentience, while an emerald surrounded by glass panes will make it less independent. These would be placed in the third inventory.
To enhance its brainpower, you'd simply add neurostems.
Neurostems would need to be connected via redstone dust to have any effect. Crystal focusers would need to be next to neurostems to affect them.
The final part, metal, is about machinery and cyborg..ism.
The basic part would be iron meshflesh, which is simply an iron bar (not ingot, bar) and a receptive flesh. This can be used instead of receptive flesh when making organs ("machines") or entities to make a hardier version.
It can also be used to make an integration needle; 3 iron meshflesh in the vertical center, a diamond in the top-middle, glass panes in the top corners, and a receptive flesh in the bottom-center. This will allow your organism to interact with machines, furnaces, and so on. You jam the needle in any block, and, once connected to the organism, the organism has control over it. The machines still need fuel/power/whatever, but a smart organism can manage to transport those things; liquids and items, in and out, could be handled with a single connection.
To do that, however, more items are needed.
First, storage. This would be 8 iron meshflesh around a chest, which would create a Storage Chamber. You then place the storage chambers in a hollow 3x3x3 space, with the middle being a container (chest, diamond chest, tank, etc.). The storage chamber would then have inventory space equal to 10 times that item. The inventory would be accessed in the brain, in a new tab. The organism would count the items, and instead of having multiple stacks of cobblestone cluttering things up, would simply have one entry for cobblestone, and tell you how much you have of that. Similar to AE, except you need to smarten the organism up to allow it to count accurately with large numbers.
Or you could simply stick an integration needle in a container, that works too. The items would still be stored in the containers, but the organism would have access to it.
Sticking a crafting table with an integration needle would allow the organism to craft.
The final part, the highest tier, the ultimate of Fleshcraft would then be a cyborg.
You begin with a villager in an infestation chamber, and tell the organism to make it into a cyborg. The organism needs to have access to non-biological resources, a crafting table, a furnace, and some form of electricity (if no mods are available that can provide, the organism would make a meshflesh tentacle as high up as it can, and wait for a lightning strike). Three blocks of iron, two blocks of gold, a block of diamond, a stack of redstone dust, a handful of minutes and a spoonful energy later, the villager may come out of the chamber as a cyborg. Or it may simply die.
The cyborg would be the organisms walking body. You can tell the cyborg to follow you, and you can use it to communicate to the organism in the same way you'd communicate through the brain directly (Except you can't take or give items). The cyborg could go with you as a companion/side-kick. It could also go out on its own to explore, eating and drinking to refuel itself.
That concludes, for now, what ideas I have for Fleshcraft. Hopefully, a good mod-maker will read this and become excited. And whether s/he decides to simply be inspired, or to work with me to make this, either way I'll be pleased. Cheers. :3