First of all it is a T-56 correct? The 99/01's have a 5 speed and those are each different than the 03/04.
You will need a clutch/flywheel combo that fits a T56 and a Cobra driveshaft because I think the T56 is longer than the auto's and 5 speeds. I am sure there are other things like a clutch cable/FWA/Quadrant etc. And make sure you purchase MM's clutch cable kit, if I had to do it again I sure would purchase their proven setup, instead of having a UPR cable stretch and snap on mine.
I just yesterday finished the conversion of my 99 automatic GT from the wrecked drivetrain of a 03 Mach 1 manual trans. You will have to cut out the front of the trans tunnel about 1.5" to let the shifter through the floor. There is also a riser installed (spot welded) from the factory to add about 1" of height to the floor. I haven't installed the center console yet so I may have to adjust something to get that right. I can take some pics of it if you like. Let me know if you have any questions.
I have tried to host pics but don't know how to load them up here into a post on my wifes comp. It keeps telling me upload has failed. My comp is fd up and is asking to reinstall the windows disc which I cannot find. Anyway, you can go to twistedstangs.com, look in the members gallery under the same name I use here. I have about 7 or 8 pics loaded there. I will continue to try to get them uploaded or get my comp fixed as it is easier on mine.
I should also say to all the women/wives/girlfriends that my wife was out there with me for virtually every minute helping me and learning a lot herself too. It is her car really. It is sometimes almost impossible to do things without a second person, such as threading the wiring through the firewall, engine/trans alignment, encouragement helps a lot too. Although it could be all completed by just one determined person, life is so much easier with help. It was/is fun to do and we will install the last bits (radio/console/trim cps) tomorrow. Thanks Hunny, and enjoy the ride...