1999 Jetta Wolfsburg

My sister has a '99 Wolfsburg Edition Jetta.. It's the boxier one, so it's not the "new" body style for 99.5-2000+ vehicles..

She's been having some serious problems. Thing ran great until she went through a puddle. Afterward it would not start. Found out it needed that pump thing that goes into the intake (I forget what it's called now, IAP or something like that) the sensor that's attached to that.. Replaced that, car ran fine for about a week, or two...

Then it started running rough, and stalling at 2-3 thousand RPM, and failing to go any faster than about 15 miles per hour, mostly after it rained. Previous knowledge says spark plugs, wires, cap, rotor... Did all that, car ran great.. FOR A DAY!!!!!

Next day, it ran rough, wouldn't go any faster than 15 and stalls out at 2-3 000 rpms..

An O2 has been replaced last year.., car has ~90k on it
Only other problem is A/C compressor must be bad, tried to charge and it wouldn't cycle.. Not that that should have anything to do with the engine stalling out, but whatever..

Need help ASAP as it's supposed to be a daily driver..