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This isn't a big mystery, we solved it a few months back. The boxes are tweaked. If you swapped in a factory box for reference, you'd find everything lines up perfectly and all is right in the world. We had to shim the drivers-side mounting tab with 2 williams washers to get it right. On that note as well, the owner of the car called us after a few hundred miles of driving and the pitman arm nut had completely backed off and fell off the car. He purchased and new nut, re-torqued it to the required torque and staked it to ensure the nut wouldn't fall off. Well wouldn't you know it, the nut has backed off/gotten loose 2 more times as the pitman arm has worked itself in and loose then traveled UP the shaft on the box. Every time he tightens it, the pitman arm seats higher and he gets more thread engagement.
Good Stuff.

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