I know this is an old thread but after reading it I just had to post.
Someone has their head way up their a$$.
I know its not a mustang but I just smogged my hemi ram with 4.56 gears, underdrive crank pulley, CAI, electric fan, Superchip, and headers.
CAI and headers have EO numbers. Pulley they didnt even care. fan is not a smog item so it doesn't matter. I also have real duals instead of the factory 2 into 1 exhaust. That doesnt matter since its after the cats.
As long as the tuner does not turn off anything it will pass the smog test. They will not even know its there.
Gears do not matter because the test is at 15 & 25mph within certain rpm ranges.
At 15 my truck was at 2300rpm which tells me it probably never got out of 1st because of the shifting I set up.
My brother was a smog tech for 15+ years till he moved to a shop that didn't do smog.
If you get a truck with big tires or gears just test in whatever gear you need. He had one that had to be done in 3rd for the 25mph test but it worked and passed.