I hand turned the engine until the exhaust valve started to open, then set the intake lash, then turned the crank until intake valve started to open, then set the exhaust lash.
That's probably why you had the clatter.

You should set the intake with the exhaust about 1/3 open, then set the exhaust when the intake is about 2/3 CLOSED.

Shouldn't have anything to do with the timing advance you're seeing, though.