An additional tidbit of information. When I was checking torque values for different thread sizes on the internet, I found an official looking chart from the Alma Bolt company that specified 170 ft/lb for grade 5 and 240 ft lb for grade 8 with 5/8-18 threads. That tells me that the threads on Ford axles must be equivalent to grade 8 or better.
Might be a silly question, but did you try to tighten the nut to torque specs to see if it would tighten all the way?
If it was mine, I'd be looking to replace that axle. You should be able to find a good replacement - so why take the risk of not being able to hold the torque required for the taper to do its job? I know that when I torque these axle nuts to 200 ft/lbs, that my "fear of stripping gauge" is already quite high . . . and that is on an axle with good threads!
I was faced with similar issues on the banjo in my 41 p/u . I was going to open drive anyway so I was guided to HRW ( hot rod works); they make a kit that allows the use of 28 spline slide in axles to end the tapered axle problem forever. Banjo rear axle conversion (hotrodworks.com)