My only unforeseen issue in getting up and running was that it wouldn't start without the clutch pedal switch depressed- 100% operator error. Pretty hard to find an issue when everything is working as intended!
The deepest rabbit hole I had to go down to get everything running perfectly was with cruise control. I did everything to troubleshoot except spend time on my multimeter. Took me 15 minutes to find the problem once I bucked up and started chasing stuff down. Turned out to be a simple issue of a switch panel contact not completely soldered, 2 minutes to fix. I didn't tackle that until about a month after I got onto the road, though.