Really?? I have this same thing going on -- although I primed first. In retrospect I should have sanded finer grit before even primer. I think I used 150 on the wood, then 220 on first coat primer then 320. I am sanding after first paint coat with 400 and seeing irregularities like op has.. but if I keep sanding it goes back down to primer or occasionally wood.

Getting tired of the process though.. was hoping at 400 grit that the small imperfections wouldn't matter?

Op -- what grit are you at right now?

Oh man.. now I'm kind of regretting taking this on.. decals weren't that bad beforehand maybe I shoulda left them. Far too late now lol. Onward.

Good luck OP!! Post some final pictures and how it turned out. Hoping to do mine in less than 2 weeks.. depends on this sanding process though I guess.