Complicated problem. Break it into chunks. From the program descriptions I’m assuming there is one controller so all the wires eventually end up in one place. Use a locator to locate all the pits and accessible splices. I’d start at the “first” pit (whichever one the first set of wires emerge first coming from the clock) and make sure everything in it is understood and wired in some sensible way. Start a detailed wiring diagram. If the outgoing wires change colors through a splice or any other weirdness, document it in the detailed wiring diagram so it can all be understood what is going on at the next pit. Continue moving pit to pit and adding to a detailed, complete wiring diagram. If you reach the last pit and the diagram makes sense but the system behavior still doesn’t, there’s a buried splice someplace (and Murphy’s law says if there’s one, it’s not the only one). Reassess based on the diagram and the behavior — can a work-around be figured out with what’s there. At some point, if it’s still screwed up and there’s no good way to locate where things have gone wrong, it may well be time to bury some new wire.