My Trans.Failsafe.Prog problem

[reyez]

Hey all just looking for some help

2001 3.0 x5 130k miles

Problem:
About 2 weeks ago we had some hard rain in my area of Houston, TX. My sister drove her x5 into some flood-like conditions (we're talking probably about 6-10 inches of rain). she noticed the Trans Failsafe light had come on as well as an SES light. No water had gotten into the car, but she did notice the car shifting a little bit odd, it was shifting like she was in DS mode but the car was clearly in D mode. The following day she told us the story and me and my dad did the research and checked out the SES code.

P0103: The MAF may be disconnected, or a wiring connection may be bad The MAF sensor may be damaged The vehicle computer may be faulty (very rare)

We cleared the SES light, but turned on again right after the car turned back on. Failsafe light would turn on everytime we started the car.

What we've tried so far:
We did our research on numerous forums and found that battery/alternators seem to be a very common problem so we went ahead and got the battery replaced, it was under warranty still. Then we went ahead and took out the MAF and cleaned it ourselves.
One thing to add about the car is about 2 years ago she was driving the car and had a violent flat tire for the rear driver side tire, which led to the tire speed sensor to be completely obliterated. This was replaced ourselves as well (dont get mad but we just duc-taped the wire instead of buying a housing for it).

As for the way the car drives now, its still as if the car was in DS mode, theres no problems starting up the car, no shaking, and shifts through all the gears. SES light still on, Failsafe light still on.
any ideas?
I'm hoping that we wont have to replace the alternator