I chose paint first
I painted first. Here's how I made my decision--you may have a completely different set of criteria. I don't believe there is a right answer--do what works for you.
1. I wanted my plane done. I wouldn't have considered my plane done without paint.
2. I was painting myself in my garage, so I needed to paint in pieces. I painted 53 individual parts. It would have been difficult for me to disassemble and paint.
3. I don't believe that it is possible to get great adhesion, especially to fiberglass parts, after they have been oil soaked, had bug guts splattered into the pinholes etc. Pristine parts are definitely easier to get a good paint job on.
4. I wasn't too worried about scratches. I painted it, I can touch it up. I built this thing to fly though, not win awards. That said I have one awards and get compliments on the paint often.
5. I would not have been able to stand the downtime to get it painted after I had tested. Also, W&B, stall speed, speed runs, and much of the other testing done before paint will be invalid after paint. I enjoyed test flying, but it just hurts my engineer's brain to paint myself into a situation where I HAVE to retest everything.
Again, it's possible to make up an equally valid list of reasons to paint later. This was just my list.
Guy