You're just going to have to sand those bad boys out, re-paint and re-decal. I know how you feel but it's not such a disaster. If you do as good a job on the re-paint as you did initially then it'll be fine. It's the fact that all that effort and work has gone tits up that's the real bummer.
Check out my Jungle Lord How I laughed !!!

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Paint markers or any kind of marker will not work for this. You can have all the "how to" threads about playfield restoration, but it won't mean everyone can do it. There are tons of variables elements out there, that will kick you in the balls. Crap like this still happens from time to time even after doing this for 8 years. And sometimes you don't know why. Could be bad batch of clear, would be bad decals, could be wrong sealer, bad sealer, could be a reaction to the original lacquer to the decals (not in this case but does cause other wierd stuff). That's one of the main reasons i'll do waterslides over a layer of clear. Just in case crap happens, you can sand it out, without destroying all your hard work repainting everything. It sucks to have this happen. Just sand it out, seal those decals better and with a better product and try again.
Problem with Varathane (besides fading out your colors with every layer), is that it takes forever to dry. leaving a ton of time for it to react to other elements you have in play.

My problem was using a cheap, crappy, pre-catalysed clearcoat and putting it on waaaayyyyyy too thick. The touch ups were all done with acrylic. Didn't turn out too bad in the end.

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