Emission testing envolves an inspector looking under your hood and under carriage verifying that you vehicle has all the right emission control components according to your VECI sticker (The sticker on the underside of the hood). Also they will get in your car and make sure the CEL is working the way its suppose to. The vehicle then gets driven on a dynomometer where equipment collects exhaust samples making sure the vehicle does not exceed the Carbon Dioxide, Carbon Monoxide and Nitric Oxide levels, and also communicates with your OBD II system. Then it goes to the final stage where they test your gas cap to make sure you are getting a good seal, then you pay for the test, $25 every two years.
Others who have done engine swaps have had to go through a few extra steps depending on the year of the engine being swaped and/or the year of the body/frame.
The people they have doing the inspections, 80% of the time don't know squat about cars, so there is potential in getting away with things or dealing with extra headaches.
Correct. on the bumper height and mud flaps.
There is law that the head lights and fog lights be a certain height.
According to CRS-42-4-205:
"Every head lamp upon every motor vehicle, including every motorcycle, shall be located at a height measured from the center of the head lamp of not more than fifty-four inches nor less than twenty-four inches,"
Not sure the height limits for fog lights, but if you have them covered up you shouldn't have any problems with the man.