As far as I know the car will inspected as a 1966. It doesnt matter what year the engine is it goes according to the year of the car. They do not have to know what year the engine is from. I am putting an engine from a 87 Crown Vic into my 65 Fastback. Hope this helps.
After chatting with my local service station (also licensed for inspections) They suggested actually going to a state facility first to get a baseline for your emissions. The emission standards are based on the model year, and they are different than new cars, but my shop didn't have the exect specs. By having a newer engine (and hopefully cleaner than the original) it should be OK. I'm not a fan of NJ state facilities with their lack of concern for your vehicle, but it's a decent idea. (So much for my thought of going to a private facility first!)
My car is also registered as a daily driver and they go by the emissions rules from the 60s for sure. Since there is no catylitic converter it would probably be impossible for your car to meet the standards that came about later.
My 65 with a 289 passed with one idle mixture screw 6 turns out and I was only getting about 10 MPG. (2 years on the VMF have helped that situation/forums/images/icons/smile.gif).
I went to a private shop. I figured they'd let more things slide considering I was paying for something I could get for free at the state inspection stations.