I'm in trouble...

My intake pipe on my 98 Prodege was almost completely severed so I knew I would have to get a replacement. My boyfriend talked me into getting a short ram instead because it wouldn't cost much more.
Before I put in the short ram I cleaned my engine off with degreaser so that it wouldn't look so bad next to a nice shinny short ram. I then spent 3 hours putting in the new short ram. I am pretty sure I did everything right and I was gentle with the mass air flow sensor so I don't think I broke it, but now my car isn't running right. I found some water that made it into the spark plug wells when I cleaned the engine and I thought that was the problem, but I dried it out and its not running much better.
The car is running really rough and it gets worse when I put it in gear. Once I get it in gear it usually sputters out pretty quick. My check engine light is flashing too. I checked the spark plug wires and they are ok. I'm sure something I did messed up my car but I don't know what.

P.S. sorry its so long

I'm not sure what the flashing check engine light could mean..

however I am kinda concerned over the fact that you broke the intake, and cleaned it with degreaser.. if you sprayed anything like your mass airflow sensor, it might cause some problems I would think as it's not made to clean those..

and then you said you used water? (water in the spark plug wells?) by chance you didn't get anything up in the intake wet?

also I know on some cars if you get the fuel injectors wet, they tend to not work right for a bit until they dry off...

try renting a obd scan tool and see if you can pull any codes.. for the light, that should tell you where a problem is..

and it might be your car just doesn't like the short ram..