I'd been following the thread for a while and didn't realize it was a sixpack until yesterday. Have you tried disabling the outer carbs to see if you can isolate it to fuel? Does the misfire only happen under load? Or can you replicate it in the driveway? If you can replicate it in the driveway, I'd hook up your timing light just to verify a spark and go from cylinder to cylinder and also at the coil to verify everything is firing - especially during the pop/backfire.
This is a strange one...