Dave-
I can't help you with a shop, but I can give some advice based on my experience. My 68 convertible had metal work done at a reputable shop (using NOS quarters, NOS door skins, NOS front fenders - everything else was solid). The car ended up being put on the back burner at that shop for many years with no end in sight, so I took it back and it is currently at a restoration shop that really knows what they are doing. I had planned to do the same thing as you; Have the shop perform final panel alignment, bodywork, then paint the car. I would have them do the glass, conv. top and some weatherstripping & trim. I would take care of the remainder of the assembly. Should be fairly straight-forward, right? Well, not really.
The problem is that a reputable shop who is going to take responsibility for the final product is not going to take the car at face value. They will want to go over the existing work very carefully to ensure that everything was done right. Also, since the car is just a shell (I assume), they really have no idea if all the trim, bumpers, emblems, lights, grille, etc are going to fit, especially if aftermarket panels were used. A good shop will want to test-fit all those components to ensure that the car will go back together without issues after final paint is complete.
So, they will end up with all your parts to complete the body assembly. They will have fit & removed these parts at least once and know when & how they want to install each piece. At that point, you may as well just let them fit all these parts as part of the body restoration. Why risk damaging your expensive paint job at that point - just let them do it. This is going to add time & money to the project, so be prepared for it. I thought I was prepared, but I know my jaw dropped just a little when we started talking estimated hours.
