A little bit of an update: best I can tell now, I was dealing with 3 problems, all of which were tied together.
1. The Rustoleum primer and the Krylon topcoat do not like each other. As another member suggested, using the same brand of primer and topcoat definitely led to better results.
2. This battle of the brands was particularly noticeable where I sprayed too heavy a layer of topcoat, which caused the soft blisters. Using multiple light coats (read and flow the instructions!) seemed to turn out well.
3. I handled the parts too early. I let everything sit for a week instead of overnight. I can no longer scratch anything off with my fingernail.
The parts all look better now. Except they're sitting on my workbench and not on the car - that's a different problem.