Okay, adjusted cam again, set valves and ran the bike before messing with points to see if the noise dropped. Definitely sounds better. Not sure how I messed that up last time, but anyways thanks for the callout there.
Now I am rewriting for mech points and advancer. Just noticed they never removed the condensers… the solid state of the pamco should not need those. I read somewhere that this can mess with the circuit board and cause misfiring. Curious if this is an additional issue or related to the hanging idle. Going to continue with the switch to points.