Now that you mention it... you're right about the windows! I was thinking maybe it was the age of the regulators or something, and just dismissed it.
You've already built a storage/bed unit for the back, so maybe a way to access it underneath? I haven't built mine yet, so if I wanted to create a storage area below the rear floor where the tire was... (gears are starting to really whirr)...
How did you come up with an alternator from a Caddy? I used to manage a Napa, so I may be able to put my hands on a spec book for alternators. Although, I kinda like what you've come up with since it isn't much to mod it in.