I just got done doing it. The instructions at corral.net were a big help.
8.8 Solid Axle Gear Install
It's definitely not as difficult as people seem to think it is. One thing that was hard to find is what the pinion depth should actually be. A friend of mine going through the same process had an article that covered that. It's in the June '99 issue of MM&FF called "All Backed Up" on page 92. Ford uses something called the Master Housing Dimension. It's 4.415 for an 8.8" rear. You measure the height of the pinion gear with calipers and then subract that from the MHD. That will give you the correct pinion depth. Start by reusing your original shim. It's a good bet that it will be correct if you stick with Ford gears.
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351W 89 Mustang GT Convertible