I've been reading along and scratching my head, seems like you're doing a good job with troubleshooting and process of elimination.
Not knowing exactly how the modern automatic transmission was adapted, could there be trouble with that connection, loose, and out of balance or something? Wouldn't cost anything but a few minutes to pull the cover and take a peak at converter and flywheel.
You visually checked cam timing by turning crank past TDC and watching valves. Could they be off enough to matter but not enough to see? Would it be worthwhile to use a degree wheel and dial indicator, and if you lack specs at least compare to another Stovebolt.
Could it have a broken camshaft that is fractured such that it still turns but results in slipped and or erratic timing for a few cylinders?
Grasping at straws,
Grigg
