Hey Mike. I'm sure you have the same problem. They didn't actually get it fixed until I believe it was March of 2009.
To test it do the following....
Start your car
Don't put in the clutch yet but start pushing your shifter towards first gear. With the shifter pushed up there..this is really had to explain but slowly push the clutch in. If you hear a hiss while the clutch is going in it is defective.
If you have any problems let me know. If we have to we can chat on the phone and help you check it.
Yes..Ford will warranty the clutch with the pulley install and CAI. Your clutch issue is a clutch issue and does not matter on what gears are in the rear end.
Hmmm..on the harmonic noise I have no idea. I would have to hear it and check it out do diagnose correctly. Your mechanic could be on the right path. As far as I know if it is the gear alignment at some point your gears could shatter. I would have Ford check it out since it's under warranty. I have not experienced this problem.
Let me know if you need anything else.
Shellee