It really depends on the model and year of the bus in question.
What model/year of bus are we discussing?
Shuttle, Crown, IC, Ward... each have their own unique variations and engineering, often with simple fixes to most.
Many of us have extensively sealed roof penetrations, seams/laps & successfully removed/sealed our windows.
Surely someone has the same bus as you, HestiaMea. Please, tell us what you have (or a photo) so that more custom/accurate experiences can be shared.