Finally got back on the job this week. Bought the paint for the half tonneau ($200!) on Thursday and got after it today.
I decided not to use any filler on the panel, in keeping with my "messy as they probably were" aesthetic. Hit the rough spots with the Dremel, gave it a final bit of scuff, blew air on it, then wiped it down with acetone and a tack rag.
Primer is a 2k epoxy. The paint shop gave me this stuff in a spray can—just enough to cover the half tonneau. I suited up against the isocyanates.
I painted just outside the garage, then left it in the sun for an hour and flipped it to do the other side. Couple hours later and its in the garage again. I'll wet sand it tomorrow with a 400 grit block before mixing down 8 ounces the base coat, loading it into 
—and trying my luck.
Weather's supposed to be like today—75, partly cloudy, not too humid or windy.
I'll hang the panel with wire and S hooks from a Krause folding ladder in the driveway. That should give me good access to all sides.
If I'm lucky I'll be able to clear coat it on Tuesday or so.