It would be pretty simple to wire in a temp relay and give it a shot. The instructions say it should be wired that way and that's the way I wire my LC-1 with no issues. Been on and off at least 20 cars with no failures.

Not sure why it would make a difference since it has been run that way for years? During the headers and changes something could have changes in wiring? Grounds are very important.

Can you update/reflash firmware with a MTX-L ?