After quite a few discussions with various transmissions shops near me, I have come to realize there is only one (so far) who will rebuild a FMX, and they are almost 2 months out. Seeing the cost to rebuild the FMX is within 2k of the quote for the T5 setup from MDL, I am somewhat certain I'll just pull the trigger and change over to the manual now. Hoping the learning curve isn't too steep!
Those T5 transmissions are really nice. They have had a run of over 30 years in Mustangs and are very durable. You have another option available you may want to consider. We replaced our 1973 Mach 1 auto tranny (C4) to an AOD the other year, and love how it turned out. The original 3 speed auto floor shifter works with the AOD, although I did need to replace the shift linkage. Our Mach 1 has a 3.5:1 TractionLok rear axle. At 60 MPH in 4th (OD) gear we are turning only about 1,800 RPM. Very nice. And because the engine was built for street/strip it has plenty of torque to overcome air resistance at higher speeds, the OD increased our potential top end - not that I care to see how much it has been increased. I am very happy with how it turned out.
Attached are some files that contain the parts and vendors lists, plus the web addresses for the YouTube videos I posted showing the entire swap process, as well as how to adjust the Throttle Valve pressure (easy to do, and also important to do properly). The only thing I would do differently were I to do another 3 speed auto to AOD conversion would be to get a 4R70W automatic overdrive and an aftermarket tranny control module. Although adjusting the Throttle Valve pressure is not hard to do, it is tedious to set up. It would have been nice to be able to make TV PSI changes from the control module as opposed to dragging out the oil pressure gauge and connecting it to the transmission test port. I recently ordered the parts needed to install an oil pressure sending unit and oil pressure gauge to be mounted in the center vertical bezel so I can both watch the TV pressure, and to allow faster oil pressure gauge connection in the event I ever decide to further increase the TV PSI setting. I am running at 39PSI at the moment, which was done to increase the 1-2 and 2-3 upshift road speeds. That worked out nicely. Factory setting is 30 - 35 PSI, but I prefer a little more to to get a firmer upshift and upshifts at higher road speeds.
Whether you go with the T5, or an AOD, AOD-E, or 4R70W I am certain you will be pleased with having an OD gear available. Best of luck with the project!
Everything is mostly back together before I ran out of energy and daylight. I did mess up one of the trans cooler lines, so I either need to order another set or break out the tube bender. I may do a temp fix to get it back on the road next weekend. All I have left is to put the driveshaft back in place, hook up the parking brake again, and fill er with fluid once I have the cooler line issue worked out. 
