could be a few things. I did a write up on rear ends in the Wiki on the site.
1) pre-load on the pinion gear bearing
2) case spread could be incorrect.
3) Shim for the pinion nose could be incorrect.
4) gear lash could be incorrect.
5) if you have a timed gear set you need to make sure the teeth are correctly placed between the marks on the ring and pinion gear.
When the gears were changed was the crush sleeve replaced?
Was the backlash set according to the instruction with the gear set or to FORD OEM spec? you must follow the manufacturer recommendation.
If going from an original ford gear set to a modern ford set or an aftermarket set, the pinion shimming must be looked at,
you want the gear mesh center on the Heel and toe of the tooth face, and centered between the drive and coast side. if your high on the coast side and low on the driver side, with the gear set centered heel and toe then you know you need to swap out the shim, and then reset backlash and try again.
obviously the case spread needs to be redone each time, the shim is changed, this is to make sure your starting case spread is .010" that is a good ball park to start at.
here is my wiki entries:
http://www.7173mustangs.com/thread-how-to-rebuild-a-ford-9-inch
http://www.7173mustangs.com/thread-how-to-rebuild-a-ford-9-inch-part-2