In an OBD2 plug in state, you can't pass unless your vin matches the car's vin. It sucks. So yes..the vin shiould be updated IMO.
Trans cooler lines, good catch. Swapping the lines is possible as the click fittings at the radiator unscrew. The Sc car would be a thicker radiator typically, unless it's been replaced. So the rad swap makes the most sense.
The maf table isn't that much different, won't cause any issues. When the bin is updated, yes it should be corrected.
Scott..what's the reasoning behind not having the pcm control the bcs?