About 3 months ago, Trooper was leaking automatic transmission fluid (on this vehicle, there is no way for the user to check or add fluid) so I took it in for service to correct. Two weeks ago, the transmission went completely, slipping in all gears and losing fluid all over. I limped to the dealer and was advised that it needed a new transmission (under warranty!). Got the car back and I am experiencing major shuddering and some engine cut-offs at very low speed or standing still. I have gotten a "check transmission" light once. I can't wait until Monday to take it back to the dealer, so I was wondering if anyone can tell me how to retrieve the trouble codes manually by checking light flashes?? Where do I put jumpers? Etc...

Nope you can't use jumpers. Autozone (if you have one in the area) will read the codes for free.

Or you can purchase a basic code reader for 40-150 bucks.

My guess is that you have a bad Intake Manifold gasket (common on these trucks and covered by warranty too).

-Ryan