Why not use the factory GM PCM that came with engine you choose? Why go aftermarket? With the matched LS3 engine, wiring harness, and PCM the only issue will be interfacing the new engine harness with the 2002 body harness. Or verify that you can run the LS3 with a 2000-2002 LS1 F-Body PCM and harness. That would probably encounter few if any body harness interface problems. Or just get a front clip from a wrecked 2000-2002 LS1 F-Body, drop your V6 out the bottom, roll the LS1 engine, trans, harness, K-member, full suspension package under the V6 body, drop the body on it and bolt it together.
Beyond the engine, you will need a new trans (the T5 can't handle LSx power), clutch hydraulics, limited slip differential, revised fuel system, mechanical throttle actuator, etc.