I have dealt with runs in two ways:
1. Spread some body filler over the run covering a reasonable area around it, then sand 400 grit or so to knock it all down - the run will be sanded away with the filler, and you stop when all the filler is gone. Wet sand, cut, and polish.
2. Scrape (not slice) the run down with a razor blade until you are pretty even with the surface, then wet sand, cut, and polish.
There are a myriad of opinions on how to do bodywork, you'll just have to decide what will work for you, with respect to where you are at.
If I was where you are, I'd just sand 400 and re-shoot more clear. If it fails years from now, at least you have the skills and know-how to fix it then. In the mean-time, it'll work, and you'll carry on.
I'm curious to see if my paint even sticks at all to the epoxy under it.