Nearly all refined ores have reached the end of their cycle and don’t have a use outside of getting shredded back into dust for that extra .375 each. My setup was extremely simple: crusher-sluice-centrifuge-shredder-main GT barrel storage area (dusts). I do agree that those extra purified small ores are a bit of a headache, because you could indeed still have an extra bathing or centrifuging step for those, which is why before getting an item filter I would stick to processing one type of ore in bulk at a time and use a hopper screwdrived to output only multiples of 8, because a centrifuge will accept and process those 8 purified small ores as it would have accepted a single regular purified ore. Again, here large batch processing stops you from coming short (not having enough of a specific kind of purified ore and crashing your entire processing chain) if you prioritize that specific kind of ore in the first place. It’s a tricky system though, that does require some small babysitting before aluminium and item filters (or buildcraft/logistic pipes, but I’m assuming this is a greg-only setup) come into play: I would always feed the centrifuge with a stack of the already purified ore you’re centrifuging and have a backup of 8 of the ore in the hopper, this way the hopper will only accept that specific ore and never get filled with anything else as long as you have more of that ore coming in, since the crusher, centrifuge and sluice work at roughly the same pace.
Let’s make a case about copper: You have tetrahedrite, copper ore and stibnite. You dig up an entire vein and use a barrel or hopper to fill it up first with tetrahedrite, wait until the first stack (and extra 8) of purified tetrahedrite ore gets cleaned up by the and then start the centrifuge and shredder. At this point You can send a redstone signal to stop the crusher once the barrel is empty, but sorting up the remaining stragglers among the tiny purified ores is obviously gonna be a manual job, but what I used to do was simply chuck those extras in the shredder directly, since the dust will still stack in a barrel, and then repeat the process for the next ore.
Of course, in my case I eventually ended up automating the process by hooking up an extra utilities filter to re-rout filter all small purified ores into another storage for further processing, but that’s not a GT functionality.
In short, process in bulk and expect some tedium. Hope this hasn’t been completely useless!