auto 4r55e not shifting past 2nd

[vermont danger ranger]

I recently got my truck stuck in a water hole for a couple days, and subsequently had to let it dry, and change all fluids. I got the truck running today, and on the first test down the road, it ran great, shifted smooth, everything was ok. When I actually went to leave for the day, it would no longer shift past second gear. After reading through the tech section I came across a mistake I made when changing the filter. I first removed the two gold bolts that go to the valves, thinking they were parts to the filter. In the tech section it says DO NOT REMOVE THESE, or fluid can bypass the o rings and stop the trans. from shifting. But it does not tell you how to correct this problem. Please Help.