Only on bank 1? Possible injector leak could cause a misfire and black smoke due to fuel dumpage into the cylinder. If its the passenger side i would also look for a vacuum leak just in case not sure what all was involved if only a tranny swap but just imputing. Possible not a pinched harness but a exposed harness wire grounding out at times under vibration of the car causing it to touch a metal area.
1996 Mustang GT, 17x9 front and 17x10.5 cobra r replica rims, 255/40/17 front 285/40/17 rear at the moment,
o/r x-pipe flow master 40 series dump downs, cai/ram intake, 75mm c&l throttle body and plenum, pi heads and intake swap, msd wires, stock gears, untuned at the moment, no dyno numbers for now.