So.. Big engine rebuild is done. I watched the break in process and all ran fine, all rev'd fine.
Install engine in car, fresh wiring for grounding off the block, to the body and to neg terminal on battery. I noticed I was getting a small pop/misfire out of the carb once load was put on it. You can rev all day in park or neutral, once you put in drive, it pops cries all day. I do have a MSD 6AL box in the car. There is no vacuum advance. Cylinder pressures verified, timing is good... sits at about 36 on the advance. Mechanically, nothing changed from breakin stand to car..Vacuum leaks are non existent, as there are only 2 active vacuum ports. Checked cylinder head for leaks and we are good there. One for brake booster and one for trans vacuum modulator. I plugged the modulator to see if this was the issue, no joy there. I do have a B&M Star shifter in the vehicle, and it requires neutral safety switch and reverse light switch. I am at a bit of a loss to looking for this issue. I am pretty sure it is electrical. I think I am going to bypass both switches for testing to see if the shifter switch is failing. I find no mention anywhere of the shifter itself need to be grounded. It is not mounted to the trans tunnel, but on the carpet over it.

Anyone want to help with my gray hair problem?
Thanks in advance!
Drew

I agree, ignition problems are the most common. Spark can leak between crossed wires, and the MSD may aggravate that. Thick silicone secondary wires help prevent that. Carbon tracking and even moisture inside the distributor cap can do that but I'm sure you are using brand new stuff. A very lean carburetor will pop back under load. You claim no vacuum leaks but that causes a lean carb. Internal leak? Then there are the valves that may not be closing all the way. Are you using Pontiac jam nuts, or poly-locks? If poly-locks the only way to set them is with the engine idling so you can absolutely find zero lash when they clatter. I have seen guys set them statically, leave them too tight, and end up with valves that stay open resulting in backfires. They don't want to adjust them running and get an oil shampoo because their radical cam requires 1200 rpm idle and that gets the oil pressure so high the pushrods squirt like super-soakers. They used to sell little clips that covered the squirt holes while you adjusted the poly-locks. If you used Pontiac jam nuts, torqued to 20ft lbs, then the lifters are self-adjusting and you can rule that out. Solid lifters? Same as pol-locks- could be too tight. But it's OK to set those cold. That's all I can think of off hand.

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.