So I've progressed a bit further .. making soul sand and hence extracting nether quartz and a few nuggets of cobalt and ardite..
I've automated the ore extraction as much as I can.. but my only current solution is to manually move stacks of broken/crushed/dust into the packager chain when they reach a full stack.
I've made a 5x5x5 (internal) pool, partially in a river biome but no squid spawn.. endermen seem to be rare enough, but squid are non-existant, so apparently are chickens ... unless the over abundant Ocelots are eating them all and then frightening away all the wolves, unless the latter is also a biome issue.
My current problem is slimes, otherwise no sticky pistons and no import buses for the AE system..
I've also given up on the nether for the time being.. nothing useful there (ash clouds give charcoal which I'm not short of, and I have no use for sulphur clouds), and no nether fortress visible even on far render distance from my entry portal.
I've also discovered a major issue with TE3 item ducts.... they treat each half of a double chest as a separate inventory for both input and output.
My other storage issues stem from the removal of the extra-dimensional barrel upgrade from Factorization, so there is no barrel upgrade route any longer, and without a decent ender pearl supply the MFR deep storage unit is out.
Whilst I could in theory make dedicated (single item) 64K AE drives .. I have the Nether quartz to do so.. the limiting factor on doing this is the supply of redstone, it being dropped at about 1/8 the rate of nether quartz and 1/4 the rate of cestus quartz/dust.
As I suggested in a earlier post both JABBA and iron chests would make life a lot easier.. Iron chests would get around the TE3 single inventory issue and JABBA barrels are both upgradeable and portable (as are chests with it's dolly), which would make storing the wood output of my forestry tree farm a lot easier.
I also need to work out a tank solution (no railcraft tanks), and then start making fuel, to power either/both of biogas engines and/or the buildcraft electric generator, although I'm barely using the output of the 3 magmatic dynamo's I have (powering them from a bank of 8 stone barrels heated by netherack flame, it being 10% better than using a lava source block).
I'm using a vanilla cobble generator with a transfer node to supply both these 8 stone barrels, an overflow barrel, and a pulverizer to create gravel, and still can't make a significant dent in it's output....
Also, whilst I initially went the Igneous Extruder route to create Obsidian, the fluiduct lava feed into a stone barrel under a water source block (use half slabs) is about 20 times faster..
I'm interested to see where you go next with your forestry farm..