I used a plastic putty knife and Goo-Gone to clean up the old RTV stuff behind the flanges.
Was a time consuming job, but got down the gel coat and clean with time.
Used black RTV to seal new flanges, the RTV will ooze everywhere including the bolt holes when the flanges are reinstalled to transom with screws.
Some use 3M 4200 or 5200 to seal flanges. Silicon style product was good enough for MC, so good enough for me. Mine sealed fine.
PS - I was able to reattach exhaust hoses and 2x hose clamps (each) with fuel tank installed. Just some light, laying down and a 1/4 socket wrench.
1991 ProStar / 351W with 1:1 Velvet Drive