Ive thought about this and have actually sealed up a leaky sill in the past by applying a thin bead of sealant around the inside mating surface. Then you take a wet sponge and gently wet the the other mating surface. Now just let the weight of the window push down on the sealant and open her back up. The water makes the sealant not stick and once its done setting up you should have a fairly decent surface for the window to seal against.
This was on a different application, but it worked fairly well. Maybe someone will decide to be a little adventurous and try it out before I get to mine on the COE!
Jeff
