I do like the idea here, and I would definitely recomend making it independent from TE. There's a lot of mods out there compatible with RF now, so making a mod based off of just TE instead of RF in general makes it very limited.
The thing is, TE is still very early, or at most, mid-game, which is totally understandable. If that's how Lemming wants it, then that's how its gonna be. However, well...not to potentially give way to inflammatory comments, but think of it how GregTech once was to IC2. IC2 on its own didn't really offer many late-game options, except filling an entire base built entirely out of MFSUs using a massive bank of nuclear reactors. GregTech fixed that, and offered ways to use the new-found power it added to be useful, instead of just kinda there. TE, as in the mod itself not the RF framework, to my knowledge, doesn't really have something like that, something that uses what you can get from TE itself, but used to make even more powerful utilities and give you even better options.
I think adding TiCon's liquid ender would be good as a little compatibility thing. Compatibility is good. As for "machines running off nanites", you did get from the document that you actually have to physically supply the machine
with actual nanite clusters, correct? The main problem I have with in-world (non-GUI) operations is that, from what I've seen, it adds more overhead to a comparatively simple process. Its like, oh, how about IC2's macerator? You don't plonk the block down in front of the macerator and actually watch it break it down into dust. Yes, that would be very fancy, but I've got a sneaking suspicion that it'd also be very taxing on players' machines and would make automation even
more of a chore. You forget, I want this to at least loosely fit into the theme established by Thermal Expansion, but with a sci-fi/cyberpunk feel of its own.
Besides, your nanites will already be able to (with the proper clusters given and programming provided) do everything from automatically mine (think the IC2 miner, but faster and...not IC2) to farm to harvest mobs to point defense. Combine that with the amount of upgrade options you'll have to help specialize them for their particular functions like fortune/looting, auto-smelting, turning a close-range attack into an electrical jolt, and so on, and you'd have flexible minions that work perpetually, can recharge remotely (if within range and upgraded properly), and can work in the blink of an eye.
Building the brain first does sound like a fair idea, however. Maybe you'd need to jump-start the brain with a copy of
your brain's memories; something that would then be able to explain the flexibility and knowledge of your nanites. That way, they know that gold ore contains gold, they can identify it, extract the useful bits, and cast off the dross...maybe give you a 5% chance at getting a block of sand, representing the broken-down remains of the ores that have been ripped apart.