Whether you use the vinyl or not you must take care of whatever you find. Going the final step in prepping for paint isn't that much additional to do. The extra paint and materials to include the roof won't (or shouldn't) add that much more, if any, to the cost of the job. I say repair, prep and paint with whatever you are using on the rest of the car even if you put vinyl back on.
As to whether or not to put it back, if you liked the looks of it, why not? You must remember that most of these cars were pretty abused by the time we got them to rebuild. I doubt the one I bought had seen soap & water in the previous 10-15 years. A tear in the vinyl only made things worse. Do you plan to treat the car like that? Hope not. If you take care of it the vinyl can last a long time and be fairly unique today. (Insert pic of first car we restored).
Last, the idea that if the factory didn't do it, we needn't bother doing better... Let's see, factory didn't put 15" wheels on our cars, 8 3/4" rears, many V8's, Basecoat-Clearcoat, etc., etc. But for some reason we like to do these things...
