Rocker cover

I suggest the setting them while running, not because of any thermal reasons, but just because it's super easy and a lot quicker than bumping the engine over and setting valves, bumping it, etc... You just let it run and adjust. There's a video on youtube of a really cool guy doing it. lol.

Did you pull plug wires while running to specificallly pinpoint the number cylinders that misfire? I.e: 1 and 6?

Also you spun the push rods while the valve cover was off when they were released? Were any of them bent?

The other thing I'd try is if you have, say cylinder 5 misfiring, you can loosen the exhaust valve lash and see if it starts firing. It could be a burnt valve. Before I did my valve job, I had cylinder 4 misfire, and a push rod totally broke in half on 3. It still ran. But setting the exhaust lash out to about .040 Let the cylinder fire again, but it ran bad. That valve was toasted pretty good. Once it was fixed, i set mine to .010/.020 running.