Hi Steven. Welcome to our forum and Eagle ownership
A good automotive glass shop should be able to replace the glass in the window frame. If it is single pane glass, the job is pretty straight forward. Dual pane is a bit tougher.
Assuming you are going to convert the bus, you will probably want to replace some of the windows with RV type windows. There are companies that can make the frame to fit your opening. Not cheap, but the cost of replacing the stock glass will get you part way there.
Concerning the clutch, many models of Eagles have air assisted clutch linkage (see photo). I am told that it works very well. If your bus does not have the air assist system, you could probably make your own if you can find an inline valve like Eagle used.
Jim