I have a Manual trans. Replaced the clutch with exedy Mach 500 and exedy steel flywheel, new throw out bearing. New clutch setup has about 15k on it.
I have pretty much the same symptoms you have. In neutral my car has a noticeable vibration and it feels a bit as well when driving, but easy noticed when at idle. I too had the same clutch and flywheel you have installed last year.
I've been checking everything I can to get rid of it for I don't want excessive vibrations to cause any other probs. Ive thrown parts and had Ford and a performance shop check it out with no luck. My gut says it's my clutch b/c it seems to have gotten worse over time.