I would close the gap up like Tom suggested. I run the motor plate and midplate and do not have the separate ground wires to each head. If you are cranking the motor the ground should be fairly good.
But, you stated that it runs good and then after a few runs you start having the issues. How is your battery voltage? Are you running 2 batteries or 1? Are you running an alternator? If regapping the plugs doesn't help, you could possibly have low battery voltage. The MSD box takes a lot to run properly.
Does the problem go away the next time you bring the car out or do you have to change the plugs for the problem to go away? If you have to change the plugs for it to clear up, then the plugs could possibly be too cold. Have you changed the heat range after taking the blower off?
Bill M