Yeah you're definitely abusing the overflow chest mechanic there :P. Don't get me wrong, it's a clever way to use it, but it's just not at all what it's intended for... As I said before, it's really just a place to dump the items from the assembler temporarily - it was never intended to be shared between multiple assemblers at once. And again, the current way of "just stuff anything that fits into the assembler" is already quite slow and adding any kind of logic to figure out if the recipe uses that item and how much of it it needs would inevitably make it a lot worse...
With that said, I'd love to make the loading/unloading less of a pain, it's just that I haven't found any good way to do it that wouldn't absolutely kill the performance and still fit the spirit of the mod (mainly not requiring you to use any special assemblers). I was thinking I could make a second mod for that, which would focus more on the actual production, rather than playing around with circuits. It is just a couple of very vague ideas so far though, so don't expect anything anytime soon :|
As for the performance issues - I really can't do much without the save (or at least a blueprint) that can reproduce it... Seeing those chests tho, It might be what I mentioned in the last post (inserting items from large chests), which there's nothing I can really do about, since I have to go through all the slots to try and insert the item to the assembler. It's still weird if that happens when the combinators are idle though...
Also, if you could keep the two threads separate, that would be great ;)