Mine does the same thing, except mine is from 1 through 3rd gear. Yet I have no idea. More than likely gonna have to pull it out and see what is going on
Mainshaft snout is scored where the input shaft roller bearings ride on it. Usually happens when the trans is run low on fluid. Only way to fix it is a new mainshaft or find a good used replacement....and redo the entire rebuild.
It will be loudest in 1st and reverse and get quieter in 2nd and 3rd and be silent in 4th due to the mainshaft and input shaft being 1:1. Whoever rebuilt the trans should have noticed the damage. Would look like pitting on the smooth bearing surface.
Btw...ALL 85.5 and up mustang t5s are world class....even 4 banger and v6. It just refers to bearing and blocker ring styles.....nothing special.