I have quite the problem with my 2005 SL55 (722.6) transmission shifting. This will be along writeup because I have trying to solve this for a week.

I am located in Ohio and two weeks ago we had a lot of rain. I had to leave the car outside since my garage space is taken up with another project. During the rainy week the alarm went off but it sounded muted (clue 1), I thought it was just the rain finally getting to the 20-year-old alarm siren. Then last weekend I took the car on a couple of errands, total driving distance around 75 miles with several start/stops. On my way back home it wouldn't shift out of first or second gear. I pulled into a parking lot and shut it off then restarted hoping to get it back to my house. Pulling out of the parking lot same shift issues then went to neutral (on a hill no less). Shut off for 10 seconds and restarted, made it about 2,000 feet and again went to neural, several more shut off and restart cycles got me in my driveway. It threw a check engine light P0730, incorrect gear
I found wet carpets on passenger side and traced back to HVAC air inlet overflowed into passenger compartment. I cleaned muck from air inlet and got it working again. To dry the carpets, I ended up pulling the passenger seat and running a fan to dry everything, this took a week. I inspected the TCU and Central Gateway, no corrosion, no signs of water damage. I inspected all the wiring under the carper, no corrosion, just foam saturated with water.
Put it partly together and went for test drive, same problem drive a little bit and it will just go to neural, stop and shutoff 10 seconds and I can go a little further. I hooked up DAS and no errors or events in the TCU and no errors or events in Central Gateway, ECU shows P0730 active and stored.
Next I sat in driveway with DAS hooked up and monitored gear selected and actual gear. Again at first start works good for 2 to 3 gear shifts, that is I shift to reverse it goes in reverse. After 2 to 3 gear shifts it will show the proper gear being selected but actual will be neutral, and still no error codes (I did this several times)! Also it never went into limp mode.
So troubleshooting so far, inspected ECU and Left Sam, no sign of corrosion or water, lifted carpet on drivers side and it is dry, pulled the transmission connector and it is dry. Swapped out TCU, I had a TJ Mary tunned TCU and put back in my stock one (original to the car). Transmission oil looks good, I have changed it within the past year. Also checked right SAM no sign of water.

I am out of ideas, I keep thinking it has to be water related since that is when the problem occurred and I had the strange alarm. I really don't understand why the TCU will not store an error even though it recognizes that it is not going into the right gear. ECU will store an error so clearly the ECU can see what gear the TCU is calling for and that doesn't match the actual gear. Also it always works after shutdown and restart. I don't shut it down long enough to cool down so it isn't heat related. It is like something reboots.

 

I wonder if you shouldn't have a good look at the shifter assembly in the center console. I'm not sure how it 'talks' to the trans, but I'm guessing it's electrically via the TCU. That kind of moisture inside, even if it didn't touch the shifter, can wreak havoc, as I gather you understand given you trouble shooting so far.

Let us know what you find.