Welcome to the forum
Bus windows tend to be very leaky and drafty and are extremely poor at thermal management.
I happen to dislike the look of RV windows myself.
I'm personally planning to install regular house style windows in my bus post-roof-raise, with tempered glass, double pane, etc etc. Basically, the best windows I can possibly afford.
With a roof raise, you have the ability to pick out the window sizes you want, and then put in a metal frame to carry load around the window. You can install a wooden frame within the metal frame, and attach the windows to that. House windows assume a traditional 2x4 stud wall, so there needs to be some extra work done to mount that in a thin bus wall, but those problems are easily addressed.
I personally recommend that you stick with a safety or tempered glass. Here in Virginia, it's a legal requirement, but I don't know if it is where you live.
If you do put back your original bus windows, then you'll want to try to duplicate the original framing as much as possible, and do your best to eliminate any leak potential.
You should start a build thread and document your work, and share pics! We love reading about conversion projects here and seeing the progress.