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From talking with Georg(@orangefj45 ) and reading another thread, the process starting in 2019 became a LOT more problematic compared to old days.
First issue I saw in your initial post is wanting a 5.3L with a manual transmission. In Calif, that is like finding hens teeth. I'm not sure if CARB/Ref have issue with reusing same vin on tunes for swap engines.
Second issue I've read is CARB/Ref want class equivalent swaps; suv to suv, car to car, light truck to light truck. Car into suv is no longer considered valid. This issue further screws up your desire for a manual transmission. FJ6x is considered suv. I can't think of a 5.3L suv that came with a manual trans.
The big issue now days is CARB/Ref want ALL computers for OBD2 engines that are on the CANBUS in a donor car to be on the target rig; this is things like anti-lock, body computer, air bags, wheel speed, transmission, etc. They don't care if the engine computer actually uses any of this info or not.
Somewhat related to the above is now the ref is somewhat bypassed on OBD2 swaps. The whole swap is scanned from the PCM into the Calif database. From what I read, this is now permanently available and Calif can in the future use that information to flag your car if they decide to change the rules again.
OBD1 is somewhat easier because of none of the CANBUS stuff.
*EDIT*
Here is thread that is discussing swap where a guy posts his recent experience:
Passing CA Smog Referee with Toyota 3.4 Swap
www.pirate4x4.com
The local REF here rejects ALL 5.3 swaps due to GVWR from what 4-5 others have told me. Several have tried and NO DICE. Sounds like the REFs get a manual, read it or go by previous learning/dealings and then enforce what they comprehend/want to. I'll ask next time I'm with him on the 5.3. I know smog shops here are failing rigs with aftermarket long range tanks here now as well. Had this happen to two of my customers. Had to completely remove the tanks on both.
Also, if the O2 sensors are not within schematic design (+/-) 3" its an auto reject. If an OE cat assembly that has a CARB EO# has been cut and extended, auto reject....
Getting crazy and I live in the RED13/Jefferson State area of NorCal.