One possible problem (and I have mentioned this before, with out much comment) with the SI PCM and emission testing is the OBDII system monitor readiness test. It is rumored that PVO disabled several monitors and if the test detects more than 2 monitors not ready then it will fail the functional portion of the test, 1 for 05'. This is not just CA, many states have adopted this test and some only require this test and do not even test tail pipe emissions.
If you remove the SI PCM then you had better do this several weeks prior to the test so the monitors can be set properly or you will fail.
I do not feel that you would need to remove the SI injectors on the 03's since these are the same injectors used on the 04's. It is my guess that DC had a lean fuel condition better solved with larger injectors than with PCM programming(High RPM Mis-fire TSB?) and the PCM should have no problem adapting to the injectors. Again, you need to drive the car to allow the PCM to adapt prior to the test.
Just my 2 cents worth
