No tranny expert here but my reading leads me to believe the problem with adding new ATF is that it will loosen old gunk in the tranny. This stuff will then lodge in new places causing new problems.

Therefore, FWIW, I would first do a thorough flush with new ATF. Drive around to give the new fluid enough time to loosen the old gunk but not enough time cause a problem, maybe 30 minutes max.???. Come back and fix whatever is wrong, replace the filter and refill with new fluid. At that point I would probably think I got almost all the old stuff out. However, being semi-paranoid and for a few bucks in fluid and filter I would probably drive around for an hour and do yet another filter change just to make sure all the old junk was gone. I would install the new pan gasket with this second filter change. Again, no guarantee just what I would do unless someone clued me in otherwise.

I would not continue to top off with new fluid due to the potential of new fluid causing new problems. Also the potential of losing a tranny due to not fixing a known problem is also not my style.