Awesome, that's good to hear! As far as I'm aware you need separate sides with the TE3 machines unless you're using Factorisation routers. On the plus side even a stone pipe will extract so it's not that costly.Does the item sink still work if it isn't directly connected to the furnace?
It looks like the problem got fixed in version 0.7.4.dev.89. That's great and I was even able to load the save that kept crashing the game BUT now I have to use 2 sides of the furnace: 1 with item sink and 1 to extract the stuff. Isn't there a way to do both with the same pipe using the same side?
For compact setups I'd have basic logistics pipes for extraction (so they're smart about where the items go) and a single router with a speed upgrade to insert ores into the furnaces and an itemsink or supply pipe going in.