i own a 95 eldorado but im not a big fan of the vinyl top as its getting worn out and starting to pull apart. Is it possible to delete this option entirely as the newer eldorados have done? If not would/can a dealer replace the vinyl section with a black vinyl and guesstimation on price?

It would be a lot cheaper to just replace the to rather than remove the top. There are a few mounting points that would need to be adressed as well as the condition of the paint under the top. Go to a good upholstry or convertable top shop rather than the dealer, the dealer is way to expensive.

Yeah thats no problem, ill probably have to shave a few mount holes and repaint, but my biggest concern is the structual integrity of the back glass as it seems the vinyl section holds the back glass in.