TOTALLY agree on the classic look of the stock 4106!
I donated my 4106 to the Pacific Bus Museum awhile back for their '06 restoration project because mine had a perfectly intact rear window and they needed one. Win - Win for both of us. (My coach had some serious, I mean SERIOUS cracks where the upper rear radius rods attach to the chassis, which was the reason for the donation.)
As for the rear glass, a fellow busnut here in CA with an '04 solved a similar problem by taking the OEM glass out, then, using it as a mold, had dark Lexan replacements made by a local plastics shop. Same material as the side windows on an RTS. Because Lexan is tough as nails but scratches easily, he had it coated with something to reduce the outside scratching while being washed. Wish I could tell you more, but he has since passed away, and the last I heard his daughter's family took the coach home to TX somewhere.
With the glass out, it should be easy for any good bodyshop journeyman to solve the rust issues for you. Call in a favor, maybe??
FWIW & HTH. . .