Post CPS recall swap, transmission problems?!

[Beast1bk]

I am having some serious problems after taking my truck in for the camshaft position sensor recall from Ford. Everything was running great before I took it in. Now, when it first starting acting up, it was shifting erradically and the O/D light was flashing, I ran the DTC codes and came up with P0603 - Internal Control Mod Kam Error, and P1000 Monitor Checks not complete. I called the dealership and they told me that should not have caused any problems. I cleared the codes, put the truck back to stock, and got a P0782 2:3 Shift Error, I have put the truck into performance mode and back to stock and am still getting the same O0782 2:3 Shift error code. In performance mode I can barely drive it because it won't shift into 3rd gear until I break the 3,000 RPM mark, not matter how hard I am on the pedal. In stock, I have to really feather the gas to get it to shift, and then after getting home and checking the tranny fluid level, which came up fine, I tested putting it into and out of gear and it is really slamming going from reverse to drive.
Does anyone have any ideas? I didn't have any problems until I brough it to the dealership and actually didn't have any problems for about 20 - 40 miles after I left the dealership. Could this be a tuner problem, a CPS problem, or maye somethings wrong with the tranny? I haven't seen this problem described on any other forum, please help.