You're right about the clear coating too soon, I just learned that the hard way. Luckily if you catch it early and it's only a small spot instead of half a bike frame you can let it dry and the wrinkling really smoothes out, almost undetectable, then you can sand and repair that spot.
One thing I learned recently is the benefits and drawbacks of stripping a bike vs. sanding and priming over the original paint. I'm a clean-slate kinda guy so on one of my latest projects I stripped the frame, sanded it for surface adhesion, cleaned it with mineral spirits, let it dry, then applied my etching primer, filler primer, base coats, then clear. It all seemed like the right steps, etc. Unfortunately I DO NOT like the adhesion I got on the bare metal, or actually lack of adhesion. The clear's bonded to the color, the color's bonded to the primers, but the primers don't seem to have adhered well to the metal, even using etching primer. (I'm talking all rattle can stuff here)
In the future, if I have a bike with a good robust factory enamel coat I think I'll just sand it and treat the bad spots then etch-primer over that. Why strip off a good coat of paint that's really well bonded to the metal?