Misfire at cruise, popping/afterfire at 3000RPM

Yes even with my outboards disconnected my big cam 340 will still pull up to 5 grand seamlessly using only the center carb.
I've also run off of just the center carb in the past when doing work on the outboards, same problem. Outboards completely removed and the intake sealed off, so I don't think it's an outboard issue.

Is the rear carb sticky when being engaged by vacuum or can you feel it hanging up manually. I would do whatever I could to correct that problem because you know it's going to be a problem.
It's sticky both under vacuum and when it's being moved by hand. Doesn't open freely, and doesn't close on its own. Although I do understand that they don't necessarily close on their own -- that's what the center carb linkage is for -- the front outboard closes on its own when disconnected from the linkage.

I don't know if you've seen any of Harold Demes' videos on YouTube, but it turns out he lives about 30 minutes from me. I've been in contact with him, and I'm trying to set it up so he can change the throttle shaft bushings on at least the rear outboard. Speaking with him on the phone, he doesn't think the shaft itself needs replacing, but the base might need to be align bored.

One more thing that comes to mind and again excuse me if it's been covered have you checked top dead center number one cylinder in conjunction with your timing mark to make sure that something weird is not going on there.
I don't remember if it's been covered here or not....after 4 pages you kind lose track. But yes, I verified the timing mark with #1 TDC. That was a thought early on, that the balancer slipped.

Any thoughts on the 5/16" tank to pump fuel line vs. 3/8"? I already have the 3/8" along with the 3/8" sender, just need to install them. I don't see how a larger line could hurt, but could 5/16" line cause a lean issue? I changed the pickup sock last year when I bough the car, but not the sender or line.