Sorry to hear about the troubles with your wifes XSport. CPO does not mean perfect unfortunately.
Datalogging should be done every time you drive the car, esp if you are not able to reliably reproduce symptoms. In this case you are saying you can?
Anyway:
• Keep track of which gear the stutter occurs in. Standing start, punch from a roll, all gears, etc.
• Check the intercooler for pooling oil. It may be getting sucked into the engine.
• Check the plugs for signs of cracking, carbon deposits, oil, and/or fuel smells. Could be am injector, valve cover gasket, etc.
• Confirm the knock sensor wiring is safely away from engine.
• Confirm trans fluid level and condition.
• Check if the halfshaft recall could be applicable by going to owner.ford.com. Even if it doesn't it could be something to look at.
• Pull codes from the PCM. Not all codes will flash the CEL.
• Check and clean the MAP sensors.
Hopefully this will help identify the culprit(s).