This is from a purely hypothetical vantagepoint, as I have no personal practical experience...
Have you considered just puting the same old roof back on? In surfing around looking at such things, that seems to be a common approach. The window posts are just lengthened, more or less, by splicing in more steel. Then the extra surface area along the sides of the bus is covered with sheet metal. The back of the bus stays in place, and sheet metal is installed front and back to bridge the height between the rear and front and the higher roof.
It sure would save a lot of work over constructing (and waterproofing) a new roof.
Just a thought. It may not be suitable for your purposes.
I can tell you from practical experience that once you get into a bus project, you will be glad for every labor/time saving "innovation" you can come up with!!!
Oh, yeah, remember that overall height is going to be important to you. Not just the height of the new roof, but the height of the new roof PLUS anything up top: racks, A/C units, decks, vents, smokestacks, anything you put up there. You're probably not planning on raising it to the height of a double decker, obviously, but there are not a few overpasses, bridges, etc. in the US that are less than the 13 1/2' minimum clearance on the Defense and Interstate Highway System. There used to be a steel frame bridge with 11 feet of clearance near me, but it fell down...not really, but it was about to, so the highway department closed off the only road crossing that river for about 50 miles so that they could spend a year replacing it...with a concrete bridge with no superstructure.