Somis Duramax,

"Does this truck require several starts to clear pending codes?"

Yes, The control module turns OFF the "Service Engine Soon" Light after 3 consecutive ignition cycles that the diagnostic runs and does not fail.

The reason I said it was a fuse/wiring problem was
1: You said it had a U2106 which I knew was a Comunications problem.
2: You said the PRND2l was not under underlined..
3: You said the transmission had a Horrrible clunk into gear..

They all point to the TCM not powering up..
If the TCM is not powering up, there is no way for the PRND2L to know what gear it's placed in.
The Horrible Clunk was the transmission going into 3rd gear because without power (to the TCM) the trans will become a none Electronic trans and will resort to 3rd gear or commonly known as "Limp Home Mode...