From what this looks like, this whole operation hangs from the Molecular Transformer being in the mod-pack. Turning Charcoal into Coal is otherwise something that is impossible (I'm not sure if the new Equivalent Exchange still uses the Philosopher's Stone that can turn Charcoal into Coal).
For those who use the Monster mod-pack, you can use Coal Essence to generate your coal (from the Magical Crops mod). Please note that any type of fertilizer will not work on Magical Crops (bar Thaumcraft's Lamp of Growth, and OpenBlocks' Sprinkler). Yes, this kinda contradicts the "Apatite into Diamonds" challenge, I'm well aware.
So, for those who are still interested in my process:
Main Manufacturing Process:
Machines:
- Planter MineFactory Reloaded
- Harvester MineFactory Reloaded
- Cyclic Assember (x3) Thermal Expansion
- Macerator IndustrialCraft 2
- Compressor (x2) IndustrialCraft 2
- Plant and farm Coal Seeds, remembering to loop the seeds from the Planter to the Harvester.
- Haul the Coal Essence from the Harvester to a Cyclic Assembler, turning the Coal Essence into Coal.
- Macerate the Coal into Coal Dust (Use Overclockers to make this process faster but less power efficient)
- Put the Coal Dust into another Cyclic Assembler with Flint, crafting them into a Coal Ball.
- Take the Coal Balls and put those into a Compressor, which will produce Compressed Coal Balls (yes, really).
- Using yet another Cyclic Assembler, craft those Compressed Coal Balls and Obsidian into Coal Chunks.
- Compress your Coal Chunks into Diamonds, using the Compressor
For the automatic Flint generating:
Machines:
- Igneous Extruder Thermal Expansion
- Rock Crusher Railcraft
- Pulverizer Thermal Expansion
- Generate Cobblestone using the Igneous Extruder.
- Put the Cobblestone into the Rock Crusher, generating Gravel(100%) and Flint(10%)
- Pulverize the spare Gravel, making extra Flint.
For automatic Obsidian generation:
Machines:
- Magma Crucible Thermal Expansion
- Aqueous Accumulator Thermal Expansion
- Igneous Extruder (x2) Thermal Expansion
- Generate Cobblestone using the Igneous Extruder.
- Put the Cobblestone into the Magma Crucible, generating Lava.
- Using the Aqueous Accumulator, generate Water.
- Pipe the Lava and the Water into the second Igneous Extruder, generating Obsidian.
All of these machines could be linked using Applied Energistics' ME Cables, or Thermal Expansion's ItemDucts, or Ender IO's Item Conduits, or even BuildCraft's Pipes if you're feeling dangerous.
I understand that this entire process could be obsolete using Magical Crops' Diamond Seeds, but in my honest opinion I'd prefer to use my process because it looks more technological, and more satisfying to watch.
It also wouldn't surprise me if there was a more efficient / faster process that uses a different order of manufacturing, or using different mods (RotaryCraft, for example), but I like using these mods for a lot of things that I do, because they work with most automatic processes.
edit1: I'm well aware that this is a lot of text with no pictures, and I relish the thought that you might actually have to use your reading skills for once. >:3