Just my $0.02, but here's what I'd do.
1. Make sure you have good "short" protection with fast blow fuses, TVS suppressors, etc.
2. Resolve the issue with the switch plugs.
3. Get it running again and take some voltage measurements around the track to make sure nothing funky is going on.
4. If it all checks out, I'd keep running it. Even the best designed and constructed layouts are going to experience issues down the line which have to be dealt with - it's the nature of the beast.