How to prep roof for paint?

Prep as you would the rest of the car- if it has pits, you'll need to neutralize, high build, and block it.
My two cents: Since you're still going to have the vinyl top trim and holes, use them as the guide for masking for primer/paint. Shoot the top with Harley Davidson black wrinkle paint to simulate the black vinyl top and reinstall the trim. Regular flat or glossy black always looks too hokey to me as a vinyl top replacement. The H-D paint has a much less aggressive wrinkle than the VHT stuff, so it actually looks kind of legit.