I would just like to mention I tried building one of these myself, following the guide in the video on page 2. It worked perfectly, except when it came to putting the cells back in the reactor. Using the redstone setup in the video, the reactor came back on before all the fresh cells had been replaced in the reactor (i.e. they were still travelling through the pipes when the reactor came on). How can I make it so there is a longer delay before the reactor turns back on?
My design in the early video relies on the fact that there's an "invisible" 9-item buffer in between the reactor and the relay, which slots the cells in pretty much instantaneously. It relies on you have an extra 9 cells always in the 'circuit', obviously (ie. in the whole pipe system). The downside is it limits you to reactor designs needing no more than 9 cells. So the minute you need 10, you cannot rely on that relay holding enough in it's "buffer" to allow instant swapins - you will need to delay the reactor startup sufficiently enough for the additional cells to come down the pipes. The suggest of a counter linked to an item detector is the safest bet.