Your Pontiac Fiero might not be California emission legal after this engine change. The problem is with the transmission. The fact that you will be keeping the original transmission means the engine control computer (for the 2005 engine) is going to be missing a few transmission sensor inputs. This may trigger the check engine light on. With the check engine light ON, your Fiero will fail the smog test.
If you research further and find that not connecting the transmission inputs to the ECC does not effect the engine management system (does not illuminate the check engine light), you may continue with changing your Pontiac's engine to a newer 2005 3.8 liter model. Just make sure you use all the emission components belonging to the newer 3.8 liter engine. After the engine change is complete, your Pontiac Fiero will have to be inspected by a California State Referee. They will conduct a smog check.
The Referee will ensure that the job was done properly and that the new engine does not pollute. If all is well they will issue you a BAR label which will be placed somewhere on your vehicles chassis which will be an indication that the vehicle is California legal, and subsequent smog inspections can be performed at regular smog check stations.
We recommend you speak directly with a State Referee before beginning any work, and inquire on whether keeping the older transmission will be a problem. You can contact the referee by calling (800) 622-7733.
