Having done this job several times before, I recommend pulling the motor. It's only a few more bolts, and working bent over the fenders/cowl is such a PITA.
If you haven't tuned the new edelbrock you are leaving a lot of power and mileage on the table.
Also timing with vacuum advance will make a big difference.
Summit branded parts are usually very poor quality. I have had luck using a ratchet strap to pull on headers to move them around. Just beware that the shaft will move around in every direction, not just up and down.
If the studs were pulling out there would definitely be some new valvetrain noise along with it. I believe you are seeing the effects of mass produced parts.