Transmission will shift fine when it is cold but then will exhibit shifting issues after it warms up ???
Possible worn Servo bore, sleeve it or get a reman.
If you decide to get a reman put in, have them install a Transgo shift kit w/ warranty and be done with these problems.
http://www.fordservoboretransmissionfixsolution.com/symptoms--solution.html
~ steel servo pin wears out a groove in the aluminum servo bore
TSB 09-12-12 5R55S/5R55N/5R55W TRANSMISSIONS
- SHIFT CONCERNS, LOSS OF 2ND, 3RD AND 5TH GEAR, INCORRECT RATIO DTC'S
- PROCEDURE TO INSPECT AND REPAIR SERVO PIN BORE WEAR.
FORD:
2002-2005 Thunderbird
2005-2009 Mustang
2002-2009 Explorer
2007-2009 Explorer Sport TracLINCOLN:
2002-2006 Lincoln LS
2003-2005 AviatorMERCURY:
2002-2009 Mountaineer
ISSUE:
Some 2002-2009 Explorer, Mountaineer, 2007-2009 Explorer Sport Trac, 2002-2006 Lincoln LS, 2005-2009 Mustang, 2002-2005 Thunderbird, and 2003-2005 Aviator vehicles equipped with a 5R55S, 5R55W, and 5R55N transmission may experience shifting concerns. A loss of 2nd, 3rd, and 5th gear may have overdrive band or intermediate band failures due to servo pin case bore wear causing reduced apply pressure.