For my time and money, I would pop the pinion cage out and replace both the pinion seal and the spacer. If your unit has the "Daytona" cage, it should have a solid spacer. Be sure to check the pinion yoke for rust, roughness, and/or grooving.
Some OE ratios, like 3.00 : 1.00 are timed, and the pinion and ring gear are marked with paint. Paint marks will line up with one pinion tooth and two ring gear teeth. These must be reinstalled properly. Most other ratios are what is called a "hunting tooth" ratio, meaning that eventually each pinion tooth meshes with each ring gear tooth. These can be installed in any convenient mesh.
No, you will not change the pinion depth specification doing this job unless you change bearings, and even then it's unlikely.
I would also suggest you change the "O" ring on the cage. It's cheap.
Hope this helps. If you have any other concerns or questions, don't hesitate to ask.
Don
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