There is an excellent product called "Instagone" that will remove those stains from your headliner. It is available at most Winnebago dealers under part number 698209-05-000 and I have purchased it through some of the local hardware stores. Be sure to cover all your upholstery and carpet with plastic before you start.
I don't know if this will help but my RV had water stains in the roof where it leaked. The headliner looked like berber carpet. I took a spray bottle of vinegar and water, sprayed the stain and used an extractor to draw it out. This seemed to do the job! I would try it on a sample in an inconspicous place first. Mine did great.