The only thing I have seen close is the one on www.stangparts.net
its for swapping in a 5.0, so its going to be a bit different, but it will give you the general idea of what would be necessary. Its a big job and doing it with a donor car and doing most of the work yourself would be the only way to do it without spending a total fortune on parts and labor! If you have a mechanically inclined friend that is willing to lend a hand that will help as well. Get ahold of as many Manuals pertaining to your car and the GT as you can find, these will also be valuable. Might be easier to take body parts from your car and fix the wrecked GT!
Rick Kilpatrick, AAS Automotive Systems Tech, Alamance Community College, Class of 99. 06 5 speed manual Mustang with Pony pkg : GT Mac Mufflers, true duals with one custom pipe. 2.5" system. GT bumper cover, all installed March 7&8 2006. AFE Stage 1 CAI, Motoblue Underdrive pulley, GT aluminum shifter knob, honeycomb rear blackout panel,and dash kit installed. Roush hood scoop and side window louvers installed. SS taillight trim has been installed, new alum. GT steering wheel installed.