Tune Removal

Typically when a car is tuned, the factory tune is saved on the tuner, so it can be reloaded if needed . I am assuming that a hand held tuner was not included with the car when you bought it. If by chance it was, then it should have the factory tune saved on it an it should be pretty simple to reload it. Otherwise a Ford dealer should be able to reflash the pcm and restore the factory tune. However, and this is important, before you reload the stock tune you have to make sure that there are no other mods done to the car that require a tune. For example does the car have an aftermarket cold air intake? Most aftermarket CAIs require a tune. If you have one that does and you reload the factory tune, the car will run lean which can lead to internal engine damage. So check the car over carefully see exactly what you have as far as aftermarket parts if any and go from there.
It also sounds like the gears may have been changed as well , I would check

That sounds like a transmission issue.