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...there are a number of automotive paint solutions that will work well to fill the rust pitting on that frame.
If it were me, I think I'd strip off the primer that's on there now, and start fresh. Which is probably what you are planning.

The fork threads look ....interesting. Don't know how much tooling you have for stuff like this. I'm in Sacramento, which is a pretty long drive, but let me know if I can help with the threading or fork alignment.