One thought I had was "What did the neck come in contact with in the weeks between the wet sanding and the last coat?"

Is it possible you handled the neck with something on your hands (any kind of grease/oil, guitar polish, KFC???)

I agree that re-shooting it is probably the best route. However I would go a little heavier grit (maybe 400) and be sure to give it a thorough sanding. Not DEEP, so you risk sand-through, but ensure you get the whole surface area (not just the problem areas).
After sanding give it a wipe down with a rag dampened with naptha (shellite), maybe a couple wipe downs, then re-spray.