Just make sure your roof is in really good shape before doing this since vinyl tops rot roofs. I ended up replacing my roof skin already... Moldings shouldn't be too hard to get from some of the speciality salvage yards like Mo-par City (1-800-426-HEMI) or Stephen's Performance (256-247-1332). I think the moldings around the window are the same and all you need is the molding for the bottom of the top.
What I think will be a bigger challenge is figuring out exactly where the holes are at in the body but once you have the moldings and lay them in place, that may work itself out too.