Clutch Trouble, Please Help!! Need advice on correct parts!

I bought a used 07GT. The guy I bought it from said it had a Fidanza Alum. Flywheel and Spec 3 clutch. I was having noise issues and the pressure to use the clutch was hard on my knee so I bought a Fidanza 2.1 clutch kit and a new friction plate for the flywheel. Well, a friend was installing today, turns out the flywheel is still the FoMoCo stamped steel flywheel. He resurfaced it since I could not run out and buy a new one. He installed the clutch and took it fro a drive. The clutch is not fully engaging. He was doing research on modularfords.com I think and said people were talking about having to shim the flyweel to get full engagement. Is this true? If I get an alum Fidanza flywheel overnighted to have him install, do I still need a shim? Is there a new throwout bearing I should get for the complete install to be safe?

Please help, car is sitting at his shop until I can get parts to fix. He is going to have to pull the tranny again, so I want everything to be right.

Thanks!!