so over the weekend I guess I had a little too much fun playin in the mud and now Im paying for it. I went through some pretty big holes (4 ft deep) and everything was fine... till the next morning. I woke up and went to run to the store and My tranny was in "limp" mode. I only had 2nd and 3rd gear. No OD and no 1st. It also clunks really hard now when shifting into any gear. I pull the codes using my scan gauge and do some research. well this is what I have

P0876-UD PRESSURE SWITCH SENSE CIRCUIT
P0888-RELAY OUTPUT ALWAYS OFF
P0988-4C PRESSURE SWITCH SENSE CIRCUIT
p0731-GEAR RATIO ERROR 1ST
P0732-GEAR RATIO ERROR 2ND

I changed the realy out hoping that would fix some of it, and it didnt. I changed the fluid and filters in there because I did end up with a little water in the tranny. Wasnt a bunch, but just enough to make it a little milky. Now I'm at a loss on what to do. Any ideas or help would be appriciated.

Oh yeah, the hold I went through, was about a foot of mud and 3 ft of muddy water.
also now that I changed the fluid, I dorve it around the block and it was slipping a little bit. so I check the fluid level and was about a quart low, topped it off and rove around the block and no more tranny and there was smoke coming out of the dip stick.

2004 QC 1500 5.7L 139000 running 35" tires.