Any way you cut it, I can't see it being cheap. There are inside skins, outside skins, electric, ribs, etc. Plus, I doubt highly I would even venture to a dealer for something like that. My first choice would be the factory. I would guess $3000 to have an aftermarket dome put in. I would question how well an after the fact would stay sealed, knowing that even the factory installed units leak.
I come up with that price based on a recent interaction with the factory on a request for swapping out a 13.5k unit to a 15k unit. I figure they average $600 for the A/C units which meant that the factory wanted about $1k to put it in (if I picked up the 31 footer I was looking at). There it was a pretty even swap out, with little to no modifications to the roof, compared to what you are talking about.
I'd shoot the factory a question on it and give them your VIN. It may take a few weeks to get a quote, but at least you'll know and you'll also know it would be done as right as it can be....
Computers manufactured by companies such as IBM, Compaq and millions of others are by far the most popular with about 70 million machines in use worldwide. Macintosh fans note that cockroaches are far more numerous than humans and that numbers alone do not denote a higher life form. -NY Times 11/91