I found this
Since Ford sets the stock ring and pinion to the correct specifications for your particular axle housing, the easiest way to set the correct pinion depth would be to measure the stock pinion head with good caliper and see what the difference is compared to the new pinion head (for example purposes lets say the stock pinion head measures 1.600") . Also measure the stock pinion shim and record the thickness (for example purposes lets say it measures .025"). Example, if the stock pinion head measures 1.600" and the new pinion head measures 1.597" you need to add a .003 shim to the new pinion to bring the total thickness of the new pinion to a total of 1.597"+.003"=1.600" and then add the stock pinion depth shim of .025" before you press on the new bearing. So now you have 1.597" + .003" + .025" = 1.625" which is the same as the stock pinion depth of 1.600" + .025" = 1.625" and should be right on! Second example if the new pinion is larger, lets say its 1.603", you need to "remove" .003" of thickness. We can easily do this by decreasing the thickness of the stock pinion depth shim. So we subtract .025" - .003" = .022" which is our new pinion depth shim! So now the new pinion head thickness of 1.603" + .022" = 1.625" which is exacly the same as our stock value of 1.625". If you can get new Ford Racing gears for your 10.25" axle, the pinion head thickness should be exaclty the same thickness and so all you would need to do is repalce is the stock pinion shim of .025" with a new .025" shim just so you have a new depth shim under there (remember the .025" is for example purposes only). After this the only thing you have to worry about is setting the correct back lash and carrier bearing preload. The easiest way to do this would be to put shims on your carrier housing so that the carrier fits very snug in the axle housing, adjust the backlash to specifications and then check the pattern. Once you are satisfied with the pattern, you need add an equal amount of shim thickness to both sides of the carrier to give proper bearing preload, this will not mess up your back lash . Over all, I think it should be just like rebuilding a 8.8" its just that the 10.25" axle
Hope this helps, if I missed something please let me know.
That is one of the best ways I've heard that explained.