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Pinion Set Up Methods
Pinion Depth:
Pinion Depth determines the wear pattern between the Pinion and Ring Gear, and this determines whether the gears whine or not, not to mention how long they last. Obviously, it is pretty impairative that the depth be set correctly on a new set of gears. In the final analysis we will use white gear marking compound to check the wear pattern on the new gear set. However, we do want to get the pinion set up as close to specifications as possible beforehand.
From the factory, 8.8 rear ends were set up with a pinion depth of 4.415". Our goal is to duplicate this with our new gear set if the gear set is made by Ford Racing Performance Parts.
(As an observation I cannot understand why anyone would want to install another brand of gear in a Mustang rear end given the track record of Ford gear sets and the selling price of $149 from Diversified Product Marketing.)
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On the left bottom are three calibration tubes for setting up the dial indicator (4", 3", and 2")

Laying horizontally at the top is the "piece one" which bolts to the bearing cap mating surface

Next to the calibration tubes is "piece three" which holds the dial indicator

The red piece furthest to the right is "piece two" which connects piece one to piece three

A wing nut which connects pieces one and two

Below the wing nut is a collet which screws into piece three, through which the dial indicator is mounted

A nut used to tighten down the collet and hold the dial indicator firmly in place

Three extensions which screw onto the tip of the dial indicator (4", 3", and 2")

And the dial indicator on the top right
Pro Form Pinion Depth Set Up Tool
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On the left is the dial indicator that came with the Pro Form tool. Notice that the extension screwed into the dial indicator completely crooked. On the right is a dial indicator that I had purchased previously. The extension has screwed in properly. For a tool that is supposed to measure tolerances down to .001" this is not very confidence inspiring.

It is possible that I received a bad indicator with my kit or that I cross threaded the extension, but I wouldn't bet on it.
  1. Shimming the new pinion head to equal the measurement of the factory pinion head and shim -
This is the method that I think makes the most sense - if you are installing Ford Racing Performance Parts. After removing the stock pinion gear from the housing you would measure the thickness of the pinion head and shim with a dial caliper. Then you would measure the thickness of the new pinion head. Subtract the latter from the former, and you come up with your pinion shim thickness.

For example, you measure the factory head and shim and find a measurement of 1.975". You then measure the new pinion head and get a measurement of 1.945". By subtraction you find that you need to use a shim which is .030" thick. Put that sized shim on the new pinion and take another measurement with the dial caliper to be sure you reach the stock number.

If this method is used, pay particular attention to the wear pattern measured with white gear marking compound after installation.
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Measuring pinion head and shim thickness with a dial indicator
  1. Reusing the factory shim on with the new pinion head -
On the mustang message boards this seems like a popular choice. If you choose this method, either by default or on purpose, scrutinize your wear pattern when checking with gear marking compound. For what it is worth, using method 2 above, my Ford Racing Performance Parts 3.73 pinion gear used the same sized shim that came from the factory. This also produced the proper wear pattern.
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Pro Form Pinion Depth Set Up Tool