Hi Rchop....looking at your pics of the crank brought back an old memory (all of 'em being old at this point). First, a question.... are those marks just on one side of the crank journal? If so, this may be brinneling like we suffered with Honda CL450 back in 1971-72.
Seems the "batwing" tank paint was kinda' unpopular (on those Scramblers) and sales tailed off....just when the dockworkers went on strike on the West coast. Honda wound up unloading bikes in Ensenada, where they sat on the docks (crated) for MONTHS! Electrolysis set in and Brinneled the crankshafts where they were resting on the bearing rollers. I had to change a few cranks, when the bikes we sold started knocking within the first couple hundred miles!
If your engine was sitting in a wrecking yard, for a long time, that could be what happened. If that is it, be aware that Brinneling due to electrolysis goes deep into the dendrice (of the crystalized iron). The crank can be hard faced and refinished, but polishing (only) will not last.
Hope this helps....or I could be completely off base!! That's how it works on this site.
Regards, anyway, JimL