FYI..Which flywheel do you have
 

Most know this but I thought I would throw this up for reference.

There are different 'bolt' flywheels that came on the 99-04 2V 5-speed cars. There is a way to tell which one you have without pulling the tranny. You can count your cam cover bolts.

11 cam cover bolts = 6 bolt flywheel (Windsor engine)
13 cam cover bolts = 8 bolt flywheel (Romeo engone)

This obviously does not apply to the 4v cars because they were all 8 bolt.

From Rob's post below...

Although it doesn't have a flywheel, I figured I'd add that automatic Mach1's have 6-bolt cranks.

all the 5.4 2v's came with 8 bolt flywheel also

Not sure about the 96-98 cars, but

99-00 Windsor motors have 8 bolt flywheels
01+ GT have 6 bolt flywheels
Bullitt's--6 bolt flywheels
Mach1--auto have 6-bolt flywheels
Mach1--5speed have 8-bolt flyweels
All Cobra's have 8-bolt flywheels

good tech...basically, the '99 production year GT has the 8-bolt flywheel. All other 4.5 GT's have 6-bolts. But check the cover-bolts above if in question.

And around March 2001, Ford started using a Tremec 3650 trans in place of the T45 (in the 4.6L GT). The T45 used a 10½" clutch and the TR3650 uses an 11" clutch (on stock flywheel).

so which is the better engine the windsor or the romeo? btw i didnt know any of that thanks for the FYI

Are they all steel or did any of them come with aluminum?

03-04 cobras are aluminum. All others are steel