I had a clever idea on how to stop the reactor perfectly without resorting to crazy timers [cos I was going to use an ~5000s clock as well].
The new buildcraft 3.0.0 has gates... if there's a re-enriched isotope cell in the chamber, send redstone signal
Should work flawlessly for 9k+ reactors... not so much so for < 9k And buildcraft pipes hook up with redpower tubes decently which will work fine for the input side.
Was about to test it when I had an unexpected explosion which caused massive lag (I thought Buildcraft had a severe leak).
Though, 3.0.0 is in alpha so, probably a lot of people won't use it til it gets more finalized.
Well the timer isn't THAT crazy... It's a 100s timer feeding a 50ct counter.
Regarding your comment above about only 50% or so becoming re-enriched... I just made an interesting discovery.
I was watching my reactor inventory when my 5000s timer ran out. All 20 DI cells lost their progress bars at exactly the same instant that the reactor shut off (so that part works perfectly).
However... They didn't become RE U-cells right away. After that point, it appears that there is some random delay before they're "done."
So, two back to back half-runs should yield 40 RE U-cells, but I might have to take them out and toss them into my production reactor for a few seconds to finish them off (it's a fairly conservative 500EU/t CASUC design, so it can handle a little extra heat easily).
In any case, for this design, once you start it up, it's hands-off. Another (accidental) side effect of this design is that when it's got all the cells in (which generates 20 heat/sec, even when the reactor is off) it's perfectly heat-neutral with the cooling system off, so you don't have to rush with pre-heating. Put 5 buckets of lava in, and it will sit at 10020 heat until you start it up, and get up to about 11020 before the first water bucket gets there. Then just drop two in manually to get it back down to 10k. It also has some pistons that allow it to be configured for 1h/s positive, neutral, or 1 or 3 h/s negative on the fly.
Edit: Design as run for this test: http://www.talonfiremage.pwp.b…=1b10101001201521s1r11r19
Also, .schematic link added to OP