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I know you said you replaced most of the ignition components but you verified you have spark? Swapped plugs and wires? Before you pull the heads you can remove the springs and stroke the valves in the guides to see how they feel. You could also see if they were bent. Have you done a basic compression test? Did you inspect the rockers very closely to see that they were going down at the same rate? Is your truck cursed? LOL
I do not like the idea of adjusting the valves with it running. I would re-adjust the valves with the engine off. If it still runs poor double check your plugs and firing order. If they look ok, do a compression test on all cylinders.
Ok that is not an actual leakdown test. The Schrader valve in the compression gauge will hold the pressure. Perform an actual leakdown test. A good engine will be less than about 12%.If you don't have or want to buy the tool you can make your own out of an old spark plug and an air compressor hose fitting. It's not very accurate but if you don have a valve that's not sealing you can air the air escape out the intake or exhaust.
Josh is correct the compression gauge will not show you leak down except for what's in the gauge. What does the vacuum gauge read when you 're driving it?
Don't give up yet! Hang in there you'll stumble across it sooner or later. I'm a little skeptical on the valvetrain geometry theory. I would think that it would affect all cylinders and tyically too long or short of pushrods will increase valvetip wear and side load the valve guides. The only problem with press in studs is that they can pull out with higher lifts and spring pressures. Have you checked to see if that's the case? On the other hand that's a pretty sharp truck...would you deliver to Michigan?