There was probably a little more going on than just the reversed between IGN 1 & 2. As best we can tell, the modifications were working OK until the other night. I'm not saying it was good design, but it worked and now it doesn't. So we're missing something(s).
That's not a bad location for the Petronix. At least its switched on/off with the ignition switch. If it drew a lot of current (like an MSD does) it would eventually be a problem, but my guess is that it doesn't. (There are 3 versions of Petronix. If you want to check on power needs, see if you can ID which version it is.)