KirinDave, how fast does it output? In my early testing with TC3 it was easy to build up a huge backlog. It would never outright deny more input, but it took quite a while to get through it all.
It's slightly faster than the blulectric furnace when it has 2 bellows (I'm limited by how few deserts I can find nearby for now, chicken soulshard should fix this), and can admit a variety of input types which creates much less backlog. For my current non-quarry output this system is hugely faster than my old system. The biggest problem with naively chained TE pipelines is that it's challenging to not create severe pipeline delays due to the freebie byproducts.
I need to test more carefully, but it was my impression that the furnace has a FIFO queue it works through
by type, not by actual item admittance. So if you put in 5 iron, then wait a sec then add a gold and iron, it'll output all 6 iron before moving to the gold. But if that's wrong, chalk it up to a late night. If that IS the behavior, that's fantastic.
Another benefit of this system: you get the smelting experience. With the increasing importance of enchantment books, this is a pretty big deal. I can only imagine how insanely high my ore yields can get using elemental pickaxes and whatnot if I can also wire in Factorization's crystalizer to the pipeline. I managed to make a fortune II repair elemental pickaxe last night and I am clutching that to my chest mumbling and coughing in my cave.
I would not hook a quarry up to this system yet though; I'd probably build another furnace AND make an outlet for cobble cooking and glass cooking using more conventional means since there is no benefit to running those through our system.