It's actually not uncommon for the K0/K1/K2 bikes to have crooked frames: I got one like that from Honda on my first 750, a K1. In the extreme rush to build to meet the demand in those days, a lot of "little" things like these got overlooked.
The steering head assembly was built in a jig, then set into another jig where the cradle tubes and backbone tubes were shoved in, and the center member sections slid on. Then everything was spotwelded together and the frame removed from the jig for hand finishing. My K1 was dropped after the spotwelding process and the spots broke, then it was welded crooked. In production, they ovalled out the lower right engine mount hole and the engine's hole, so the lower bolt could go through. The only evidence of this was a small flattened spot on the bottom of the right boss where the dropped frame hit the floor. When I got it, the wheels tracked a little over 1/2" apart! It was this flattened spot that finally won the proof with the Honda reps and they traded bikes with me for my current K2, for about $150 difference.
Many of the Showa shocks came in up to 1/4" different lengths, which can tilt the swingarm, especially if the bushings are phenolic (they squish, and are soft after years of grease). In addition, the centerstand is NOT level or even, almost none were: the rounded feet that sit on the ground are not even jig-bent.
So, in short, true up these frames with levels and plumb bobs and blocks against the bottom frame rails before attempting to measure a skewed frame. They are not easy to measure: I've always used the "are the wheels in line?" method, myself.