Small update, all the photos I see of trucks with CJ3 manual climate control still use the same rear climate controls.
GM Parts websites note that it may need programming, but I believe they are the same unit. (variations being seat heaters or lack of entertainment system)
The rear seat audio control must send HVAC settings through LSLAN. There is no actual HVAC wiring going to it. It may need programming since some temperature sensors are not present in the manual HVAC version.
Here is a list of what I think needs re-pinning. Some wires aren't used, and probably don't need to be removed, but I have listed them as well..
----------------------------------------------------
Auto to Manual HVAC (-CJ2 -> +CJ3)
J2-1 (RD/WH) -> J2-4 (HVAC BATT)
J2-8 (BK/WH) -> J2-3 (ground zone 18)
J2-9 (HVAC AUTO RUN) -> J2-2 (HVAC MAN RUN)
J2-15 (BKLT GND) -> J2-10 (BKLT GND)
J2-14 (L-GN) -> J2-15 (LOW COOLANT switch) ('08+ models only)
J4-6 (GY/BK) -> J4-5 (LOW REF)
J1-19 (GY) -> J1-18 (RR MOD MOT SIG)
J1-18 (PK) -> J1-8 (PAS AR TMP SW SIG)
BACKLIGHT (Must Add)
+ (BCM MBEC)BKLT -> J2-1 (HVAC LED BKLT)
DEFOG
J2-10 (WH) -> J2-8 (RR DEFOG RLY CONT PWR)
----------------------------------------------------
UNUSED WIRING
TEMP sensor
-J3-1 (TN) DAT floor LT
-J3-11 (TN) DAT floor RT
-J1-16 (TN) DAT Panel LT
-J1-17 (TN) DAT Panel RT
-J2-16 (D-GN) air temp com lo ref
-J2-4 (L-GN/BK) OAT
-J1-4 (D-GN) in air temp sens sig (PCAT)
-j1-1 (WH/BK) pas air temp mtr (PCAT)
HVAC solar sensor wiring
-J1-15 (L-BU/BK)
-J1-5 (GY)
-J3-3 (PU) RECIRC DR PSN SIG