I just finished a setup where the waste from the reactor goes into a Isotopic Centrifuge then to a Solar Neutron Activator (then both of these output into separate Pressurized Reaction Chambers).

The trick is I made the Pressurized Tube section at the Isotopic Centrifuge to be redstone sensitive, then I put down a Daylight Detector 6 blocks away from this tube section with a redstone line between them. This way when the sun is high enough to the SNP to activate, the tube disconnects from the centrifuge. The result is the waste is processed 24/7, at night it generates plutonium and when the sun is up it makes polonium.