The biggest source of lag is the Ex Nilo Crucibles generating all your lava. Try and reduce your lava requirements by using alternative fuel sources.
As far as alternative fuels, in my next run I'm going to attempt to use MFR's biofuel with biofuel generators and/or compression dynamos as my primary energy source as soon as I can, until I get a reactor going. Biofuel gens give 160RF/t while compression dynamos are pretty long-lasting, so with the right mix you get decent power for low cost.
What I've been doing elsewhere was testing to see which things will ferment in a BioReactor. Basically: saplings from all four vanilla trees plus rubber trees, potatoes and carrots, any vanilla seeds, mushrooms (red or brown), and any dye. With the amount of bonemeal and lapis you can get from sifting, combined with the amount of food you can get from a right-clicking AA farm, plus saplings from various tree farms, you should have little trouble keeping the BioReactor filled with enough different items to max its production (if necessary, you can also get bees going and then pick flowers to pulverize and cactus to cook for dyes). Just remember to lock it with redstone until you have the inventory filled properly with enough backstock to keep it running, since item transfer nodes (and thus the rationing pipe) are not available. That way it won't use up an entire stack and end up filling with the wrong item.
Unfortunately, TE itemducts don't send different items once a given network is backstuffed, so you'll have to either build a really wonky duct setup, or get AE going quickly in order to put a pair of interfaces or precision export buses on the BioReactor's sides. Thankfully with AE going, you can feed multiple BioReactors with little trouble. If you place a TE portable tank one block away from the BioReactor, you can place a comparator pointing from the tank to the BioReactor. When there's fluid in the tank, the comparator turns on, shutting off the BioReactor. This is useful for automated flow control, as you can then confirm that you have fuel, and shut off the BioReactor early on when you might not have enough materials. Alternately, you can place a block after the comparator, then a redstone torch on the block, to turn off the BioReactor when you
don't have fuel -- or use that trick (comparator switching a redstone torch) on a chest feeding the BioReactor, to turn the reactor off when you don't have
supplies.
People love their mod-based engineering, but sometimes vanilla Minecraft has some incredibly useful bits in it even with all these mods. I like to use a redstone setup mixed with a PRC to switch ExU solar generators on and off as they fill up or the sky gets too dark -- even better, use rednet with a CC computer for finer control if you've installed ComputerCraft.. but don't forget the comparators and a light sensor, or you can't read the status of the generators and light level for your system.
