This does sound like its most likely drivetrain related, or transmission, not engine, I am going to move it there.
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.