A school bus roof is an awesome thing. Very strong, smooth, shiny, easy to clean, fireproof, rot resistant, mold resistant, did I mention very strong? Same can be said for the side walls. When you remove the interior skin you are significantly weakening the structure of your own personal roll cage. Nothing you replace it with will be as safe and sturdy as the original. Whether you are driving down the highway or parked under some trees. you might want to think about that.
The bus is engineered to provide safe transport for children in todays crazy traffic. The ceiling does not have boards and bookshelves attached to it because these things will become dangerous missiles in an accident. The floor is bolted solidly to the coachwork and will not fall on your head when the bus is upside down. The windows, doors and roof vents are multifunctional assuring safe egress after an accident.
There is this widespread perception that we have to destroy the structural integrity of the bus to own a "proper schoolie" I couldn't disagree more.
I bought a bus because it was precisely what I was looking for, a high clearance vehicle, tough and durable to drive and camp safely in. I have to stoop a little because the ceiling is only 6 feet tall but that would be amazingly tall in a passenger car or a tent! Also if the bus were taller it would certainly restrict the campsites I can use.
My best advice is to drive your bus until you are really comfortable with it, by then you will know what modifications you want/need and how much time and effort you are willing to sacrifice.