I actually discussed this with a few coworkers on how to best get it to work. I initially planned on doing something crazy with timers, but in the end came up with a pretty simple state machine approach.
Haven't gotten around to compact it yet, but i will see what i can do there tomorrow.
To start the whole process in the first place, 40 U235 are placed in the steel box just below the centrifuge. U238 is picked up from the left side belt.
After the enrichment process, the residual U238 is disposed to the top via filter inserter and reinserted. The belt content on the top is read and fed to the inserter on the left, which only activates if the top belt is empty. This prevents U238-clogging on the output side
The resulting 41 U235 from the enrichment are dropped to the right (2 Inserters for better visuals, just my style)
The bottom inserter system consists of 2 stack inserters for reinsertion and 2 fast inserters for dropping out the single overflow U235.
Green Wire reads bottom box content (bx1) and transfers info to both blue inserters (b#1 above it and b#2 left of it) as well as the two stack inserters (s#1 next to belt, s#2 next to centrifuge) resupplying the centrifuge.
The red wire goes from upper box (bx2) to b#2
b#1 is set to stack size 1 and activation if bx1 contains zero U235
s#1 is set to activation if bx1 contains 1 or more U235
s#2 is set to activation if bx1 contains zero U235
b#2 is set to activation, if the sum of bx1 and bx2 equals 41 U235 (the values get summed since both red and green wires are connected to b#2)
consider all boxes empty and the centrifuge spitting out its first product of 41 U235.
b#1 and s#2 are currently active, but since bx2 is empty s#2 cant do anything.
b#1 will grab the first U235 and drop it into bx1, consequently disabling itself and s#2, but activating s#1.
s#1 will start taking all U235 on the belt (40 left) and drop them into bx2.
once all residual U235 is in bx2, the overall count in boxes reaches 41, activating b#2.
b#2 empties bx1 and the single U235 is piped out of the system to wherever.
since bx1 is now empty again, b#1 and s#2 are activated (first step of this procedure), but now bx2 has 40 U235, which are now transferred back into the centrifuge.
I hope this explanation is somewhat clear
Edit says:
made it more compact and stackable. Process is the same, but box1 got replaced by a belt and b#1 and s#1 are now the unloaders.