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let me give you some notes from my q&a session with my local referree...
1) if the engine came with an electronically controlled automatic trans in the donor vehicle you have to use that trans in your conversion body. manual transmission (if the PCM says it is a manual trans engine) you can use your conversion car's transmission (the 911 box).
2) if the donor engine is from a car 2003 or newer you need to use the donor vehicles gas tank "or" retrofit the 2003+ fuel tank pressure sensor to your conversion vehicle's tank (2003+ gas tanks have pressure sensors to help with evap emissions)
with this in mind your best option might be to do as follows...
proceed with your LS conversion but use an LS1/LS6 engine from a camaro/firebird/corvette with a manual transmission/PCM from 1997-2002. get the conversion certified by CARB, and then change out for the LS3 down the road (since it will bolt in/out when the conversion is already done).
they will plug into the PCM and check its VIN and look for error codes and "deleted features", they might check block/head casting numbers if they can find them, so you need to really squeeze within the rules for the inspection. after that...just be smart about your mods.
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