I don't believe you should fill to the top hole, the rear end fluid should not be filling up the tubes to the wheel bearings.
I believe there should only be about a 1/4 of the tube filled with oil, making it the lower hole.
That's probably why you were able to use so much fluid.
I would call Ford Performance!!!
Look how big the AFE is and I only used 5 1/4 quarts.
And that site glass needs to be just filled with oil and it's pretty low on the cover.
And I have topped of the diff twice now almost finished the sixth quart.
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Should we ever meet the beer is on me! I drained off 2 qts of oil using bottom hole. Then I looked at my broken bolt and saw I could get a flat tip on it and managed to get the broken bolt out and replaced as well. It’s perfect now.