Ripped, here is how I see it. First you have to decide what your expectations of the car are. I know you have put a LOT of time into it. Painting it apart and reassembing it after painting is not a big deal as far as chipping and what not. OR it is a BIG deal, depending on how well the parts fit before and how easy it was for you to pull them off and on. Some cars this is no big deal, with all original panels, a 67 Mustang is pretty easy. If you have some repro fenders and stuff this can turn into a nightmare.
On late model cars like a Honda or a late Chevy pickup we paint them all apart and put them together without a hitch 99.9999% of the time. On earlier cars, I have found it really depends on a lot of things. One 65 chevelle the panels fit pretty good and you can pull a fender off and on without a problem, another one you fight to fit it and you just want to leave it there.
On your Mustang there are no inner fenders to mess with, it all comes off and on pretty easy. If this is a metallic color, without a doubt I would say jamb the parts and put it together.
Jamb behind the fender and quarter extensions and bolt them on with a pile of washers behind the studs to hold them off the body so you paint around the edges real nice. After it is painted you remove the washers and install the little rubber gasket on the edge and bolt them on and they look nice and detailed that way with a perfect color match.
On a nice driver, jambing it and bolting the panels is usually the way to go in my book. If your painter does things right there is barely an edge on the jamb and it can be cut a little and polished to almost be non-existent.
Painting a car all together and all you have to do is bolt on chrome and such can really be a lot of fun. While bolting together all the panels with fresh paint on them can be a nerve wracking experiance. We are all different. If you feel that it may be that pull your hair out nerve wracking experiance, you are probably right. And jambing the car first may be the way to go.
I do know that all the part should be on when it is blocked. Once blocked and any FINAL primering is done, THEN take the panels off for jambing. And for goodness sakes tape off the outer body when it is jambed. Don't let them spray the jambs and let the overspray go out onto the body outside. This can create all kinds of problems. Just simply tape it off and jamb pretending the outside is already done. That way you have ONLY primer on the outside to sand after it is all together.
On the subject of blocking or letting the shop block. This is a real toughy, if you say "It is all done, shoot it", by God they will do JUST THAT. And if there is a flaw, even if they PUT IT, they will say "YOU SAID TO JUST PAINT IT". However, if you say, final block it and before you shoot it be sure it is right, THEN they are responsable for how the car looks, not JUST the paint.
Believe me, I have seen it happen a LOT of times. You give the car to them "all done" ready for paint and their looking at it like ALL they are going to do is shoot it, be damned what the thing is going to look like.
I picture the guys sanding it out in the shop and one guy finds a funky body line or pin holes or something and asks the other guy "Should I fix this before we shoot it?" And the other guys says "No, the boss said we are just sanding and shooting it." And there you go, something that could have been fixed in a few minutes BEFORE it is painted will be staring you in the face every time you look at the car!
Let them be responsable for the job, not just the paint.