What about the seals? Seems like every time a window is removed or replaced
the seals are never as good as they once were. Should I replace the rubber?
I may not have a choice there they're so old.

Removing the seals makes for a much better looking paint job. I have a lot of experience with replacing seals on Bay window buses, limited experience on Vanagons. I have replaced the windshield seal on a Vanagon, and despite what I thought going into it, it was more difficult than doing a Bay. I've never had any problems with any replacement seals. You may be thinking of most other types of cars, especially American, where the glass is basically glued in. Every time I've had glass replaced in an American made car, it leaked. Always have the replacement seals in your possession BEFORE cutting out the old ones-only to find that a seal has been on backorder for months when you try to order it.   Jeff