You need to find a way to suck the water out from the top. A shop vac with a crevice tool might work, as would a large syringe with a piece of tubing on it. Changing the oil in the tranny wont fix it, the water around the gear shifter is in a separate place, sealed from the internal oil. Just suck out as much as you can, then blast plenty of wd40 all around inside the housing, then reinstall the shifter/boot...