"Where the sealer was sprayed I can see a bunch of scratches from the sand paper. There are no scratches where there was no sealer"
Yet another reason I don't like sealer. As stated, probably the best solution is to lightly sand the base with 600 wet and reapply a few coats. (just be sure the base you have can be sanded, some brands will cause you a lot more headaches if you sand them) If that is a problem, You could also go ahead and clear the panel, then after the clear cures, 600 wet and then base/clear. The clear in this scenario will seal the panel to prevent lifting or adhesion problems if you base cannot be sanded. Problem solved. The other option is to sand it all, reprime, 600 wet the primer and base again. Several options, you choose the course of action you feel best suits you needs.Hope this helps.