FWIW, Regal is spot on with his description/suggestions in terms of using a setup bearing, leaving out the crush sleeve, and this can be a tedious process.
I'll add a couple of items to make this go easier. Take an old pinion nut and grind or cut off the top (locking) section so that it can be easily removed multiple times without scarring the pinion's threads. Do all gear pattern setup without the crush sleeve (ALWAYS) and without the pinion seal installed.
You might already be aware of this but I thought it is worth mentioning that your carrier preload (side to side) should be at zero. This is found via setting it up within .003-.006 of clearance (via dial indicator) and then adding/adjusting carrier shims for however much clearance you have.Don't preload the carrier bearings beyond .001-.002" or you'll be at this again.
IMHO, the best way to complete this process is with a pad of paper and right down each attempt's results and recording the exact shims and locations at each point. Presently your pinion has too much shim. As Regal mentioned, take out .003" and recheck, and repeat as many times as necessary until you see the pattern identify that the pinion is too shallow (not enough pinion shim), and then go back to the previous shim amount. Regal mentioned 3-4 times in out and this is tedious. TAKE YOUR TIME (not yelling, but rather emphasizing) and don't be scared to put it together and take it apart as many times as needed - the worst time I've ever had was with a pinion that had to be cut at the inner bearing to be used in a different housing (thank you to GM's H-body housing) - I had that pinion in and out a dozen times before I got it correct - it took me a good 8 hrs to get it completed.
Good uck - Jim