I have no experience with this problem, but if it were me the first thing I’d do would be to drain the transmission case of all the water contaminated fluid. The accumulated water will wreak havoc while in there. After that I’d do as you plan and get it out of the weather, then remove the shifter rod if you can and put a big overturned bucket over the transmission to protect it. Then fix that windshield gasket. Others will come along with more accurate, detailed information on how to properly remove any residual water and what to do next.
