Recommend adjusting the transmission bands: Adjusting bands is a 20 - 40 min procedure you can do with an inch pound torque wrench. With a 140K it probably needs to be adjusted and may help resolve the shifting issues at least.
There are two adjustment bolts with lock nuts on the drivers side of the 5R55 transmission. They have square ends with lock nuts. The front one adjusts overdrive; the rear intermediate gears. First, mark the bolts with a line across the face with a silver marker so you can tell position when it is turned.
All you have to do is loosen the lock nut; then using an inch pound torque wrench and the proper size socket torque the bolt down to
128 inch pounds (~ 10 foot pounds).
Then using an open-ended wrench back the bolt off 1.5 to 2 full turns (latest update is 1.5 turns) and last keeping the bolt from turning tighten the lock nut to
40 ft lbs.
In Summary: If you end up doing the band adjustment, it's, loosen the lock nut, tighten the center bolt to 10-15 ft/lbs, back off 1.5 turns, then tighten the lock nut to 40 ft lbs while holding the center bolt to keep it from moving. The number of turns was in debate for some time but the latest info is 1.5 turns. DO NOT let the center bolts back out too much or you could end up dropping the seating surface of the band. If that happens you may not have any other choice but to drop the transmission, pull the TC and Trans Pump to gain access to the bands themselves and reseat the adjustment bolts. (
borrowed from Mustang Forum).
If you don't feel comfortable with the procedure take it to your local mechanic. Shouldn't be too much for them to do it for you.