What a hassle! Very sorry to hear this. Have you tried removing the window? I have removed a front window -- never a side window. For the front, you unscrew it all around, lift it out (a two person job!), reapply butyl caulking tape all around, and then screw it back in. Not sure if the side window is as easy . . . .
2012 Fun Finder X-139 "Boondock Style" (axle-flipped and extra insulation)
2013 Toyota Tacoma Off-Road (semi-beefy tires and components)