My process:
- Media blast to strip and see all the issues
- Epoxy primer bomb entire car
- Metal work
- Finish rest of the custom changes/do full mock-up
- Body work entire car, starting with bottom and secondary areas like inner finders, etc.
- Final paint bottom, secondary areas, interior, jams
- Final paint top
This way you don't have to stress about any finished paint while you are doing mock up and it makes the paint setup/prep grouped together.