Those quarter windows were one of my major headaches reassembling 2511. I feel your pain.
like you, I trimmed a bunch of the gasket that would not be visible and hopefully that made things a little easier
I taped everything together with duct tape. Gently hit a rubber mallet on a piece of wood that fit snugly into the window channel.
also drilled a hole to allow a Phillips screwdriver to serve as a prybar.
hope these help you out.
Larry