Regarding the trunk leak problem. I re-sealed the rubber lip that surrounds the opening. I pulled it off, siliconed it really well, and its been bone dry since.
I would be wary of a worn transmission. I would take it for a LONG drive (with some highway and some stop and go) on a hot day and then pull into a local mechanic. Check the temp of the tranny, and look for any signs of leaks on the underside of the motor/trans.
Also check EVERY electrical accessory and try every window