If the engine was OK before it injested the slug of water, some connection probably got wet. Your car is in the age bracket, however, for a failing RPM sensor. If it is bad, the engine won't start at all but it will run ( like crap) as it is in the process of failing. The insulation on the wire starts falling apart and it could have got wet I suppose but it is pretty well protected back on top of the bell housing. I'd check the wire plus the connection up on the firewall. I believe a new one is ~$28. at FCPGroton. If it is the problem, follow the instructions in the FAQ's CAREFULLY! You want to avoid breaking the holder at all costs or you have really big problems.

bl