Ford 2003 Mustang Workshop Manual page 2914

15. Remove the input shaft bearing cup and the countershaft bearing cup.
16. Using the special tools, install the new input shaft seal.
17. Using the recorded end play measurements, select and install the appropriate shims to achieve
the proper end play. Install the front input shaft bearing cup and the front countershaft bearing
cup.
Lubricate the bearing cups with petroleum jelly.