GM-GMC: Chevy s-10 Possessed?, good rain, charge battery

Question
I have a '99 S-10 ext. cab (automatic trans) Two days ago it began acting very strange. As i accelerate from stop, it does not seem to want to shift into 1st, until i release the accel, then it upshifts. Same thing for second. After reaching 3rd, it feels like it is going to stall. Also, sitting at intersection with foot on brake, truck feels as if it is straining to move forward. Will take foot off brake and will eventually idle to 40mph (no accelerator). Check engine light on.

Only thing out of the ordinary was we had pretty good rain a few days ago...did manage to flood the thing out (momentarily, but within 2 min was moving again [poor electrical charge, battery light on most of day) Doubt if these are related.

Any help would be most appreciated (before i mistakenly invest thousands of dollars to get it running right again])

Answer
Michael,
 
   Its sounds like you transmition has gone into "Default Mode" Basicly designed to get you were you are going with the least amount of damadge to the transmition. It will basicly raise the idle and lock out 1st gear, start in 2nd etc....What it means is that the control module for the transmition saw a fault in a sensor or component that it believes to be damaging to the transmition. Believe it or not, but the water could be the problem. Moisture in one or more of the connectors for the transmition can cause high resitance in circuits and set trouble codes in the module. Probably the best idea would be to take your truck to a reputable show and have them "scan" the vehicles modules for codes, clear them out and road test the vehicle. Any codes that re-set need to be dealt with, but if the problem was moisture then they may not reset and you would be on your way. Hope this helps