First question first... swapping the transmission with a manual should not effect the smog check. As far as the original 4-speed automatic transmission is not wired to the engine computer it should not cause a smog check problem. If the required RPM to wheel speed ratio is correct (while the vehicle is being driven on the dyno during the emissions test), you should be fine. Always check with the State's Smog Check Referee's office before beginning any work.
Upping the compression on the other hand will be a problem. California will consider this an emissions system tamper. Regardless of whether emissions are lowered or increased by this action, your Pontiac will not be able to pass the smog test with such an engine modification.
In reference to the catalytic converter... Since the implementation of the STAR smog check program, smog stations are being very careful in ensuring vehicles are equipped with proper/required catalytic converters. The smog check technician will check your vehicle's catalytic converter EO numbers. If they don't match the required CAT EO numbers for your vehicle will fail the visual portion of the smog check as an "emissions tamper". If the EO numbers are missing, the CAT will fail the inspection.
A pre-OBD II (pre-2009) converter can pass the smog check as long as it was installed before 1/1/09 and you can provide the smog station proof of the installation date. If however the installed CAT was not manufactured or approved for installation on your vehicle, it will fail the smog check regardless. The following is a PDF by C.A.R.B. explaining the new California CAT law.
www.smogtips.com/Aftermarket_CAT_ARB.pdf
