Here is a link to the Winnebago roof inspection procedure>>> http://www.winnebagoind.com/resource...%20Sealing.pdf
You can also find the link in the Winnebago section of this forum. Look in the Winnebago Service Tips sticky. It is listed in the 2010 tips. It has an excellent cross section of the roof joint.
I just inspected my roof this year. Of the ~60’ of roof joint, only ~16’ was good. That was an eye opener.
A sharp paint scraper works well to clean the old caulk off of the fiberglass skin and the aluminum roof rail. Purdy or Wagner scrapers work well. I sharpened my scraper with a file.
My roof rail joint was pretty dirty. I used soap and water on the roof first. Then I cleaned out the old caulk with the scraper. I used the scraper to run paper towels down the joint to clean out all of the mud. I followed this up with paper towels wetted with isopropyl alcohol.
I did buy the Winnebago recommended urethane caulk. It took two tubes to do my roof.
After completing the job, I read one post where the fellow used some window screen spline shoved down into the bottom of the joint to force the fiberglass skin away from the roof rail. This allowed him to get more caulk into the joint. I may do this if/when this joint fails again.