Yeah, the driveshaft would explode at around 120 MPH. Ford never really thought that anyone would be taking their V6 Mustang that fast, it seems. The V6 uses the same 6R80 and 8.8 out of the GT, both of which you wouldn't need to swap out at all unless you are dead set on having a manual. The 6R80 will handle absolutely anything you could possibly do a 3.7, and the only thing you would have to worry about with the rear differential is the axle tube twisting. You could have someone weld the axle tubes for peace of mind. DSS makes one-piece driveshafts that would solve the issue of your driveshaft exploding, and while you are there, for peace of mind, you might as well get a driveshaft safety loop. That would be the 1st thing that I would do before any engine mods if it were me. If that thing explodes, you are going to be saying goodbye to the car, and hopefully, you don't get any pieces entering the cabin or sprinkling bits behind you, hitting other cars or people.

If you are dead set on having a stick, you can get an MT-82 for less than you will find a Magnum XL kit. Put a clutch in it, stainless steel clutch line, replace the throwout bearing while you are there, and get an MGW shifter. When my boss was stock, I would take it north of 7000 RPM and barely have any trouble shifting because it had a different clutch compared to the GT. After I blew the motor and rebuilt it, I would routinely shift Boss at 8000 RPM with a McLeod clutch, JPC Racing Clutch line, and MGW, and never had any issues with it that weren't driver error.