I have a shuttle as well, but with an aluminum shell, and I deleted all the windows in the rear half and covered with 1/8” diamond plate aluminum sheet.. not super cheap but looks real nice and doesn’t oilcan like regular sheet.
We had three windows that would be covered by closets and the shower. Rather than removing the windows I painted out the glass on the inside and sealed the glass real well with automotive caulk. I used some paint meant for glass that I bought at a craft store. It's a two step process - you paint on a bonding coat first then the color coat over that. Unless you're fairly close to the bus the windows all look the same. Two of the windows in the picture are blacked out.
So I agree with backing the opening with plywood. If you can overlap a few inches on the inside it with give your repair more strength. I would use resin and structural cloth to bond the wood to the glass on the inside. The outside can be done as others have advised, with resin and cloth. You should invest in some fiberglass rollers to smooth out the cloth as you apply it. Good luck
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