Wonky wiring or not, for now I am leaving it that way. Need to work on some other things, as this issue has taken up too much of my time already.
Need to get the headliner fixed, A/C, install power windows and the paint job.
If it keeps running the way it does right now, I'm not going to mess with it, albeit it does bother me, as it isn't the way it was meant to be.