I appreciate your knowledge in troubleshooting my build but I keep thinking that this amp was fully operational for almost a year prior to my trying the speedball upgrade. It wasn't until my hand slipped and shorted that the LED's went out. Is it possible that the 250 V capacitors would be the culprit?
No, there's absolutely no possibility of this. A blown cap will short, and a shorted cap will blow its insides out all over the place immediately. This will also drag your high voltage rail way, way down, and yours is still just fine.
What wires would I have to replace? Are we talking about rebuilding the entire amp?
What I would suggest is getting a wooden chopstick and poking around the 9 pin socket and the small Speedball board with the amp on. You may find a spot where you can tap with your chopstick and suddenly the LED on the socket that's out lights up, and this can be used to direct your efforts.