hi sage;
it looks like your big bubbles are being caused by wrinkles in the glass. that's a very sharp corner on a curve and the glass just doesn't want to lay down and stay put. i think you will find that those bubbles are high spots now that the epoxy is cured. i would drill a tiny hole in either end of the bubble and inject epoxy into it with a syringe until it's full. then do your fill coats and sanding. if you sand right through the glass over those high spots feather them out and patch them with a scrap of cloth. i don't think a seal coat would have made any difference with the bubbles.
hope that's helpful. daren...