Try loading the race tune, disconnecting the battery for 10 minutes, and then drive the car.
Might give that a try today.
Not to spread voodoo, but here's a service message floating around regarding harsh downshifts (looks like it's for the 6R60 auto transmission)... not sure if it's applicable in our case or not, but just FYI:
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Clear TCM keep alive memory (KAM) and adaptive tables.
Using IDS:
Open Toolbox.
Choose Powertrain.
Choose Reset KAM.
Then Choose TCM.
Using PDS:
Choose all Tests and Calibrations.
Scroll down the menu and Choose Reset TCM KAM.
NOTE: FOR PDS, RESET TCM KAM IS NOT THE SAME AS CLEAR TRANSMISSION ADAPTIVE TABLES, WHICH IS UNDER THE POWERTRAIN - TRANSMISSION MENU TREE.
NOTE: UNHOOKING THE BATTERY WILL NOT CLEAR THE TCM KAM. IT IS CRITICAL THAT TCM KAM BE CLEARED PRIOR TO RELEARNING THE ADAPTIVE TABLES FOR THE TRANSMISSION.
NOTE: DO NOT CLEAR THE PCM KAM.
Verify that the transmission fluid temperature (TFT) PID is above 175° F (80° C). If it is not at 175° F (80° C), drive unit approximately 3 miles (5 Km) to reach temperature.
NOTE: TFT MUST BE AT 175° F (80° C) OR ABOVE BEFORE PROCEEDING TO STEP 5.
NOTE: PERFORM ADAPTIVE SHIFT STRATEGY LEARN ON LEVEL SURFACE ROAD.
Drive unit to perform adaptive shift strategy learn.
a. Accelerate from rest with light throttle to 15 MPH (24 Km/h), remove foot from accelerator pedal.
b. Brake very gently to a complete stop (allow at least six (6) seconds).
c. Repeat steps (a-b) five (5) times in the dealership parking lot or similar setting.
d. Accelerate from rest with light throttle. The 1-2, 2-3, and 3-4 shifts occur at engine
speeds between 1700-2000 RPM.
e. Continue to accelerate gently to 50 MPH (80 Km/h) or the 5-6 upshift.
f. Brake gently to a complete stop and hold foot on brake for at least ten (10) seconds.
Repeat Steps (d-f) a total of three (3) times.
NOTE: THE HARSH BUMP FELT WHILE BRAKING TO A STOP WILL BE IMPROVED. HOWEVER, SEVERAL DAYS OF DRIVING MAY BE REQUIRED FOR THE TRANSMISSION TO FULLY ADAPT.
WARRANTY STATUS:
Eligible Under Provisions Of New Vehicle Limited Warranty Coverage
IMPORTANT: Warranty coverage limits/policies are not altered by a TSB. Warranty coverage limits are determined by the identified causal part.
OPERATION DESCRIPTION TIME
082404A 2006-2008 Explorer, Mountaineer 2007-2008 Explorer Sport Trac 6R60 Transmission: Check DTCs, Reprogram The PCM And TCM, Includes Time To Clear KAM And Perform Road Tests, Authorization Decal Not Required (Do Not Use With 12650D) 1.0 Hr.