Hi and thank you for your time reading this. I have a 1990 Jetta 2D Gas (its a 1.8 i believe). I recently had to recharge the battery on it so I left a battery charger on it over night (under the car in a safe, dry place) with the hood open just a small bit. Of course it pours down rain that night and the next morning when I go out to start my car it starts up very rough, with almost a "pulse" coming from the engine (im not sure how to describe it.. its a rough sound but repeating in pulses or bursts.. your typical "that car needs fixing" banging type sound). Thinking maybe its just an early morning roughness I drove to work and back (i know laugh.. about 4 miles roundtrip). When I got back home my car did not seem any better from when I started it in the morning. Looking through the engine I noticed that over the night water had gotten into the engine compartment (the hood was left open a bit for the battery charger wires). I opened the air filter housing to find a half soaked air filter. Quickly I replaced this with a new one and traced all hoses running from the air filter compartment out and didnt find any indication that water had been sucked into the engine or elsewhere. I am not a mechanic but do know a little about cars. Any help or other places/parts in the engine to look would be a great help.
Thank you. Mike