I don't normally suggest TE for this sort of pack, but if you do, the Phyotogenic Insolator might be a good solution theme-wise for crops/agriculture.
I've still got the issue of how you get the original seed/crop. TE is included but recipes will be tweaked behind moon exploration and unique ore gen there (I think at this stage). Always possible to give the PI as an HQM reward. One "issue" I have is that I haven't been able to eliminate all dirt. I've "nuked" about 99.9% of it all, but there can still be some, if you find it. That I'm happy enough with, as that's a reward if you explore (or get lucky with world gen).
Will take a further look at the PI and what can be done with it.
Tech tree is being designed as Multiblocks as Tier 1 (Immersive Engineering, Railcraft, Tinkers*, Forestry & Buildcraft), once you get to the moon, then you get resources that allow for "magic blocks" starting with TE (moon), then Mekanism (Mars), and EnderIO/Matter Overdrive (Asteroids) with some minor overlap between mods/tiers where suitable, and with slim chances of getting later tier resources earlier.
Somewhere in there is also MFR, possibly spread across all "tiers" dependent on block functionality. TE & Mek might be switched around, I think TE is easier to fully automate than Mek.
* Planning something "special" with Tinkers and the construction of the Smeltery
Dead bushes are a good place to start. Figure out a way to "purify" and infuse with life to turn them into saplings.
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That meshes with one idea I had with Thaumcraft infusing, but I don't want to force Thaumcraft as the only solution. PI may be a good way of a RF tech solution, especially if it's uncraftable (quest reward only) at early game. Use the PI to "bulk" up core set of resources, then move over to the forestry farms for long duration farming.