Last year I replaced all the sealant where my fiberglass roof meets the front and rear caps, as well as where the roof wraps around over the side to the wall/roof seams. I used plastic disposable putty knives (Home Depot paint department), small plastic bristle brushes (Home Depot paint department), 3M Adhesive Remover (1 quart can, NAPA), and sometimes a little acetone on an old t-shirt. I worked slow and carefully with excellent results with no damage to the fiberglass roof or gelcoat/painted side seam.
It was recommended by the IRV2/Alpine Owners site that 3M sealants were used with success. I used 3M #5200 Adhesive Sealant with great results. Easy to apply, and then contour with a wet finger. A little fine water mist can help during that process. It can be painted, and I did (the body shop did). Never dries out, and maintains some elasticity.
#5200: Black or white. Fast cure or slower (24 hour)cure. Pretty much permanent.
#4200: Black or white. Fast cure or slower (24 hour) cure. Also great adhesion, but "removable" in the future.
Hope that helps.
Bruce & Donna, plus 2 Rhodesian Ridgebacks
2003 Alpine Coach 36-FDDS, WA, MT & OR