It depends on if the engine is a Romeo or Windsor. What year is the engine built? If you don't know that, count the amount of bolts on the valve covers, I believe Romeo engines has 13 bolts per side, while Windsor has 11 bolts per side. When we know which engine it is we will be able to tell you if the clutch is right or wrong (6-bolt or 8-bolt crankshaft).
As long as you have the clutch pedal assembly, all you will need is a clutch cable and clutch cable quadrant. I assume the 5 speed transmission is complete with the clutch fork, if not you will need one. Make sure to use a brand new Ford throwout bearing!
As for the driveshaft, online people will tell you the 4R70W (Auto) and 5-speed transmission have different driveshafts; WRONG. The driveshafts are exactly the same, the only difference is in the yoke. You will get away with replacing the slip yoke that goes into the transmission, which is 1/3rd of the price of a new driveshaft. The slip yoke for a 5-speed is about half an inch shorter and is 31 spline, while the auto has the longer yoke with 28 splines. If the money is there you might as well get a new aluminum driveshaft though, that way you get less drivetrain loss, a stronger driveshaft, and brand new u-joints.
If money is an issue, then go to a junk yard and pull off the driveshaft from another 5-speed Mustang GT. (96-04).
2003 Mustang GT
Intake & Exhaust: K&N FIPK CAI, Mac O/R H-Pipe, Custom Catback w/ Magnaflow Magnapack Mufflers.
Suspension: H&R Super Sport Springs, KONI STR.T Shocks & Struts, J&M Caster Camber Plates, Steeda Bumpsteer Kit, UPR Elite LCA's & UCA's.
Performance: BAMA 93R Custom Tune, FRPP 4.10 Gears w/ Terminator spec T-Lok.
Planned Mods: FLSFC, Eibach Sway Bars, Throttle Body, Plenum, Rims.