I sometimes talk myself through situations. If I don't, I usually end up talking to someone else about it, and end up figuring it out just by trying to explain it to someone else. It's simplest to just explain it to myself... for instance

"This is strange. The program seems to go off into the weeds when the begining of the state machine makes a computed jump after the ISR triggers just after setting the value for the program counter high register. The only thing that would make sense is that the ISR is clobbering the program counter high register, but it has code to save and....oh!"