Satodog, I do not have a remote starter installer.
After visiting the dealer again after the $2000 wiring harness diagnosis and realizing that the connector that supposedly causes the problem is located on the left kick panel inside the truck I cancelled the harness order and did the following. I took the connector block apart and used contact cleaner on it and reinserted the harness plug several times to wipe the contacts. I really did not see any corrosion on the contacts. Second I sealed the bulkhead opening where the main wiring harness comes into the interior from the engine compartment using a tie wrap to bring the rubber boot close to the harness and waterproof tape. It has been several months and the shifting has been fine. I tried again to get some reasonable response form Toyota but it is a black hole.
I did the exact same "fix" Bobo describes above and the MIL or check engine light has gone off. I too did not see any visible signs of water or corrosion, but I used contact cleaner on the connector block and all 4 plugs that connect to it. I used some zip ties on the rubber boot in the engine compartment and then wrapped with electrical tape to help seal that entrance. This seems to have done the trick. Thanks a bunch tacomaworld and especially Bobo, Maxa and Joes06tacoma for their posts.
Helpful links with pictures:
This link shows pics of junction block and engine compartment entrance:
This link has picks/instructions on how to remove the kick panel:
PS. I didn't go to the dealer, but you would think Toyota would offer a similar fix as opposed to charging several grand to replace a wiring harness.