I almost don't want to post this since I figure Reika will nerf it.
You can use Factorization routers to do this. The internal spaces in the extractors are addressable as "slot 1", "slot 2", etc.
Here are my notes on this. It is all based on the minimum energy required to run each stage. I use magnetostatic engines to run it all. Each extractor gets its own engine that is configured with the minimum speed to run the stage. I've listed power settings and the reduction gear ratios required to deal with the fixed torque of the magnetostatic engines.
Stage 1: 64KiW, 512Nm, 128r/s, 4:1
Stage 2: 16KiW, 8Nm, 2048r/s, 256:1 (16:1 * 16:1)
Stage 3: 32KiW, 4Nm, 8192r/s, 512:1 (16:1 * 16:1 * 2:1)
Stage 4: 64KiW, 256Nm, 256r/s, 8:1
IIRC the power is low enough that you can use steel gears and shafts but I'm currently using bedrock so I don't need to deal with canola.
I've got it set up into banks. Each bank handles a single stage. Each bank has two FZ routers, one for input and one for output. The routers are placed on opposite ends of each bank. They will helpfully distribute ore evenly across the entire bank.
Between each bank the routers are connected with an impulse itemduct with a servo. The servo is configured with a stack size of 1. This helps balance multiple ore types across the whole system, although you'll often get one extractor in the stage 4 bank with a stack of ~9 when one kind of ore runs out and is replaced by a second. It doesn't cause any real problem, though.
Behind each extractor is a BC gate set to emit a redstone signal when there are items in the inventory. Each bank has a single rednet cable that snakes across the gates and then across the magnetostatics. Each extractor and its associated engine get a colored channel on the rednet cable. The magnetostatics are configured to run only when there is a redstone signal.
Each stage takes a different amount of time. To keep the throughput constant, there are different numbers of machines in each bank. I'm using 2/2/2/8 and three redstone furnaces at the end to cook the flakes. The second stage 2 extractor will often be idle, though. I determined the ratios empirically. The exact ratios, using stage 1 as a baseline, are as follows:
Stage 1: 1
Stage 2: 0.5625 (9/16)
Stage 3: 1
Stage 4: 4
You could use 1/1/1/4 for a smaller setup or you could scale up.
Since each stage is running at its absolute minimum power, the entire system (14 extractors and 3 furnaces) takes about 200RF/t. And it is only active when there is actually ore to process. It takes a slight bit more to power the ME system that I'm using to automagically send Nether ore into an induction furnace (you get a slightly better yield if you do this instead of sending it directly into the extractors).
Hope this helps!
