>What are the best sources for these for price and quality? Are there
>things I need to watch out for?

I recently ordered seals from http://www.busdepot.com/
They seemed good quality and were fairly easy to install.  They are
also available from http://www.gowesty.com and others.  Just google
"vanagon parts"

>Also, the skylight,,,,What are
>my options here?

I ordered mine direct from "the skylight guy" so I could get a custom
color (blue, so I can always wake up to a blue sky!).
http://www.theskylightguy.com/

  If you want standard grey, you can get them from any of the regular vendors.