Yes I heared a lot about transmission problems on the new Mustangs. It seems dealerships all have the same answer saying it's normal. Some people fixed the problem with a shorter shifter like you suggested and others had to adjust the clutch and replace the transmission fluid to get rid of the problem.
Maybe you can test drive another standard Mustang or truck at a dealership to see if the transmission is the same. If it's not you will have a proof yours needs to be fixed.
Congratulations about your choice of a new car and good luck