Slant 6 Vibration

I'm not seeing anything alarming here, though some conditions that could cause your readings (sticking or burnt valve, cracked piston) would not be visible in pics like this. That amount of black gunk on the rocker assembly is really normal. Clean it up and assess the condition (turn-resistance) of the adjustors as per here.

Er-ruh…I'm assuming you did a proper valve adjustment before taking the head off…? If not, a too-tight exhaust valve or two could explain your rough running and your compression results.

Anyhow: at the very least, you're up for some new gaskets. It is very much worth your while to get the good gaskets for the manifolds.