I pulled and measured a wheel - They have 4" backspacing.
Looks like Longbox55 has a good eye as he thought a 1" wheel spacer might fix the issue.
I've been working with this kind of stuff for the last 20 years, when we used to sell custom wheels, I was the official wheel fitment guy

Bergman, I do see what you mean about the looks of the 3rd leaf, it's possable that it may have been swapped, possibly with a mild re-arch, to get some extra lift. The missing bolt is also an indication that the pack has been messed with. However, according the spec manual, the 5 leaf spring pack would be standard on 1/2 ton 4x4s '60-'66. The 6 leaf spring was an option, most likely for snowplow use.
I do also agree with you on a possable clocking issue with the pitman arm, which was one thing I mentioned in my earlier post. However, the wheel backspace isue will also cause the same problem. It could very easily be a combination of the 2. Fortunatly, reclocking the pitman arm is a very easy fix, only costing a little labor, and perhaps a socket and pitman arm puller.