Hi Larry,
Have you talked with the body shop about the paint job?
The most common method with TRs is to paint the fenders, hood, trunk lid, windshield frame (if applicable) and doors off the car, so that insides can be painted body color at the same time. Some shops might paint the door and fender inner areas, then hang them loosely for external painting. Better shops would then bake the paint for an hour or two, color sand and polish it up.
Now, you have already gone "non-original" by painting the inner fenders black (I did too on my TR4 last time I resorted it). So, you could finish the paint inside the fenders the same way, if you wish, then hang them for the body shop to paint the external areas. However, they will still need to be removed to install the stainless steel trim strims along the tops.
Is the paint shop going to be doing other prep work, such as block sanding the car all over to make sure panels are perfect? If so, they will need it assembled and all panels in adjustment. If not, they might give you a break if it comes to them disassembled.
One argument in favor of having the paint shop do the inner fenders is baked on paint is more durable than what you and I can usually get to spray on at home (especially in California, where painting is highly regulated). Also, you could have an "anti-chip" undercoat done in those areas.
The best shops usually prefer to do their own surface prep and priming. That's the only way they can really insure compatibility of subsequent coats of paint. They often won't give a warranty on a job where some of the paint is put on by the owner at home and they are left with just doing the top coat.
In the latest restoration of my TR4, I'm using a primer that removes easily with acetone, for just that reason. The shop will quickly be able to remove it entirely and get right down to bare metal to put on their own primer and sealer coats.
All this might best be decided by talking with the shop where you plan to have the paintwork done. Let them know you'd like to do some of the work, assuming that's the case, and get their guidance.
Lookin' good! Glad to see all the progress you are making.