Getting a CASUC above 6000 heat automatically...possible?

I've run a bunch more cycles with the auto-startup breeder, and found that the temp CAN vary slightly... it is either at 9270 with buckets disappearing almost immediately, or at 9520 with buckets sitting in it a second before going. So the syncing isn't exact... but for the purposes of this breeder it seems to be fine. There's a reasonable safety margin (auto-shutoff kicks in at 11k, reactor doesn't melt till 13.5k), so this variance only concerns me if it allows the temp to drop below 9k.

It might be an issue for an automatic-reload breeder like what you're discussing, but for the one I'm running, this desync is NOT an issue. So long as the redstone timer ticks stay within 1-2 seconds of the reactor ticks during a breeding cycle (~5000 ticks), there's no problem.

Also, out of curiosity... how exactly do you plan to swap out things the exact tick it is depleted? As of 1.337 the reactor inventory has been 'fixed', so RP2 tubes will NOT recognize a full reactor as a valid destination. You need at least one tube to the reactor, so the reactor slot must be open for at least that travel duration.

Yeah, you seem to know more about the mechanics you explained than me so i can't comment on that.
As for the odd/even cycles of timers. I haven't read a single line of RP2 source yet, so everything is based on my experience with coding in general but a timer set on 250ms means it will pass into the boundary between two redstone ticks. That alone makes me think that they have to be early/late every other 250ms passed.

But your experiences may differ so if you have more information on the subject then i am all ears because i am not all knowing. I just strive to know as much as i can about everything that interests me (and some that doesn't just in case)
There is an easy way (i think) to measure redstone activity visually though. Install Fraps (whichever works, yarr or no yarr) and record with your frame rate limited to 20 or 40 FPS (40 meaning you get 2 frames per game tick) and run the recording in slow motion, frame by frame. You can then see what is happening each game tick and each redstone tick. Obviously you need to have some kind of "control panel" where you see all signals without any added extra delays etc.