applied energestics (AE) would be your best bet here.
somewhat expensive, but thats why you can fortune3 the quartz needed. (vanilla nether quartz and an AE specific one)
it has a dedicated crafting multiblock, encode the recipie you want onto a pattern and stick it in.
if you need something smelted or otherwise processed, an interface+import bus allows you to encode an ore->dust and dust->ingot recipie thats not actually possible via crafting, put it in the interface, which tells the network to put an ore into the attached inventory, and somehow get a dust back, then put that dust into another inventory (the smelting slot of a furnace in this case) and get an ingot back, all when you request that ingot or something made from that ingot.
so in theory, you could store everything as ores, request, say, the component blocks for a GT fusion reactor, and if set up right, it will automatically grind, smelt, assemble, and craft its way to those blocks, where you can now simply remove, place, automate, and sit back and enjoy endless energy.
non GT example- an IC2 re-battery.
4 tin, 2 redstone, 3 copper, 6 rubber.
for a simple network, lets say i just have the crafting multiblock and a furnace connected.
i encode the following patterns:
tin ore-> tin ingot. this goes into the interface
copper ore-> copper ingot. this goes into the interface
3 copper, 6 rubber-> copper cable. this goes into the multiblock
4 tin, 2 redstone, 1 copper cable->battery. this goes into the multiblock.
now, if i request 3 batteries, it will smelt and craft everything needed for the batteries, then the batteries themselves. boom.
you can pull everything from a quarry into the network, you need one BC pipe, the interface, and the two/three other blocks you need to create, store, and view the take from the quarry.
very versitile setup.
look at direwolfs spotlight for AE, then at the AE wiki. those will pretty much cover everything you need to know.
