Mike; Howdy and welcome to iRV2.com
I realy don't know the answers to your questions we owned a 99 Bayside but never had a roof leak. I would suggest you contact Fleetword, I believe they still made the Bayside in 2004 and ask their folks your questions they would be the expert source on this and could also tell you what to check exactly for any other possible problems.
Good luck.