Hmm... maybe you should go to the Nuclear-Engineering-Section with it, but i will just tell you that you can shut off your Nuclearreactor with Redstone.
My Tutorial (In Signature) explains also a Bug with Redstone and Nuclearreactor, but if you just never deactivate your Coolantsystem, then you will not go BOOM.
Try the following:
... Reactor
... Transposer
... Sorting Machine
--- ... Tubing
--- ... Tubing (with colour tags)
--- --- --- --- [chest]
Have the sorting machine default to the colour red and mark all the other components found in the reactor in a different colour (eg. blue).
I'm not sure whether this will remove cells that aren't in the first slot though...
If this doesn't work... do the following:
... empty space
--- --- --- --- ---
|| --- --- --- --- [chest]
And have the transposer withdraw all items at once, return everyting but the cells back into the reactor and time some other blocks into the spaces that would've been taken by the cells. Then have a filter withdraw the filler blocks.
