From what I've seen, most school bus floors are metal/marine plywood/rubber. I don't have any experience with carpeting so I wouldn't be the one to give advice, but my guess is the rubber mat is a relatively smooth surface compared to plywood for adhesive bonding (depending on the product). You might be able to hack out the rubber and glue to the marine plywood, but you'll have to do something about all of the seat bolt holes. What are your plans/location of the bus. Are you not insulating?
Elastomeric acrylic caulk (I assume is on your windows) has a life of ~15 years. I noticed leaking before I took my windows out for the raise, and it would be a safe assumption that at least some of yours are leaking through/around the old caulk. If you're keeping the windows, I suggest recaulking them on the outside. You may also be getting drips from the ceiling emergency exits (I do).
This thread should really be in Conversion General Discussions though.