Condensation is produced in your engine and exhaust, it's not coming from outside most likely. Water coming out of the exhaust is perfectly normal. If for some reason you are getting water into the exhaust from outside, from snow, rain, etc., you might have hurt the cat converter. It's not really able to deal with liquid water, only water vapor (vapor condenses into liquid farther down the exhaust as it cools).

Your problem with running rough probably has to do with the hole in your exhaust. I'm not really experienced with Altimas (or anything with an automatic transmission) but engines are all fundamentally the same within the same emissions generations.

Anyway, the hole in your exhaust is probably causing problems with the second oxygen sensor, which is usually after the cat converter. Get the hole fixed, reset the ECU, and see if that fixes the problem. I have no idea whether the shifting problems are caused by the engine problems, or if they are separate.

Fix the things that are obviously wrong, and then see where you stand.