I had the underside, interior, and engine bay painted, and the body work done first (well, done to the FIRST shop's standards).
Then I installed the stuff on the underside, the engine, trans, all the wiring, hoses, got it driveable (without windows). Then I had the bodywork touched up and the car painted.
Well, that was a good plan (nice working on the engine bay and not leaning over the freshly painted fenders!), but alas, the bearings were pooched in short order and it all came out (putting the engine together now).