Golems you can filter what they pickup, this is enough for practically all purposes as they're nearly always intended for a dedicated task. The alternative way which I've used sometimes is build fences/pits, they can only jump one block like basically everything so fences or a 2 deep pit or whatever can also contain them, they can't climb ladders either so it's easy to get out still. You'd pretty much need fences for constraining chop golems though, I believe there is a golem fetter or something in either golemancy or automagy that can also be used but I haven't played with it so I'm not sure. As far as shards go remember to silk touch the ores, even just macerating gives 4 shards per ore, at best you can get it up to something like x5, just macerating is great though. Note that the sifter is not good though, unlike the ores with exquisite/flawed/whatever tiers of gems the ones like certus or shards that just give the normal gem or dust the sifter is inferior to the alternative ore processing chain as it's only worth 1.1x instead of 1.33x and the other method is something in the 1.2s I believe.
For distance transport of items your only options are chains of conduits/pipes, rails and carts, magic mirrors, transceivers, and quantum rings. If you don't have AE yet though your best bet is probably magic mirrors as you apparently do use thaumcraft, other then use carts or pipes at your preference.
For the void upgrade just restart minecraft, it's a bug that happens sometimes that seems to disable the crafting or viewing of certain items. Notably I've only seen it for JABBA and transfer node upgrades, it does only seem to happen after the first world I connect to though ever so restarting has always worked.
Finnaly got a decent Woodfarm+ fuel for my flight gadget from TC + Apples + Sugar (later for EnderIO fuel stuff) well and Cactus because I can 
