Right or wrong, I painted loose parts before final assembly. Delayed first flight by three months, probably. Been flying now for half a year, and it would be really, really, really hard to take it apart for paint now...
Painting the bottom of the fuselage was difficult. Being able to rotate the wings made that part easy to paint. Loose pieces that can be rotated get better quality paint jobs, not that I could prove it. Commercial airplane painters usually paint planes with the wings on, but control surfaces removed, methinks.
Phase One testing led to some minor modifications, which created minor demerits the paint job.
If you need show quality paint, it might be better to paint after Phase One testing is completed. If you just want to fly, paint it first and get it over with.
Are you going to paint yourself, or hire it out? Ask your painter what he prefers.