Someone on here made this mistake awhile back buying a 28 spline DS because they had 28 spline axles. But yes you can just pull the snap rings out of the u-joints and swap the input shafts if you mess it up, everything else is the same.
The T-5 transmissions in the 5.0 pushrods are 28 spline output as well as the old Tremec 3550s. The 96-04 Modulars use either a T-45 or a T-3650 which both are 31 spline. Unless you have a 03/04 Cobra with the T-56, then you are 27 spline GM style.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.