98 SE with 3800 NA

I have a strange problem where this vehicle periodically begins shifting hard but levels out after a couple of days. Approximately 103,000 miles.

Some mods as follows: 3" RT downpipe with high flow cat, 2-1/2" catback, Flowmaster super 40's, CAI, L26 UIM, Intense Polyurethane upper motor mounts (front & rear).

I am not setting any codes and have verified this with two different scanners.

Any ideas would be appreciated.