Also, DO NOT USE BONDO!!! Use All metal instead. It is designed to be used for seam filling and as a lead replacement. Bondo is a sponge and will rot out the roof if you go that route. All Metal is sold by US Chemical and most auto body supply stores stock it. Napa may also have it too.
You will need the right quarter windows, the back window trim, need to remove the tack welded studs for the trim clips, need to screw the trim clips to the window channel for the back window trim, need special clips for the bottom trim that are not reproduced ( source them from another car), etc. I have done it, but it was not simple. Oh, and don't grind the studs off. It will warp the roof and be damn near impossible to get straight. Grip them with a vise grip and twist them off gently. Remember the roof is a low crown section and hard to work straight because it will flex when you apply pressure to sand it. If you must use an angle grinder, use a flapper disc and do it in stages. This will minimize heat and warpage.