Thanks for the input. After months of working on this, I figured out it was and was not an electrical issue. What does that mean? OK..
I noticed the engine ran fine on the break in stand, but under load, it would misfire/backfire. I waited for night, and started filming the thing running to make sure I did not have any voltage jumps or something odd like that... There was nothing, but I could see the backfire coming out of the driver's side of the carb. OK.. That puts a little light on the subject. I assumed it was some sort of stuck valve, as the engine runs "fine" at higher RPM, but misfires at idle. Again, that can be explained, but, that not to this extent. I checked and rechecked the firing order. I also noticed during "test drives" the engine really didn't have the feel of a 461, more like a 287. It was a dog, which was extremely disappointing. I had this cam installed: https://www.compcams.com/magnum-262-262-solid-roller-cam-for-pontiac-265-455-cpg.html when the engine was built. I did some digging with Comp and found it has a 4-7 lobe swap. Pontiac V8 firing order is 1-8-4-3-6-5-7-2. Well, the firing order was wrong, so it was technically "electrical". The correct firing order for this cam 1-8-7-3-6-5-4-2.

I checked the cam gear for proper adjustments, and changed the firing order... Wow... What a difference.
At least this one is solved. After 10 years of not running properly, we are finally driving as it should be.