Water infiltrates those down tubes when the seam at the top is not completely welded shut. Doesn't take much of a hole for moisture to seep in. As there is no outlet designed into the frame, the water is trapped.
Simply drill a small hole at the lowest point of the tube where it intersects the next, and let the water out. You can treat the interior of the tubes with a rust preventative liquid, or moisture-cured epoxy primer to prevent any future rusting. Or, you can drain the tube, weld all the holes up, and then bake the frame before painting or powder coating it to dry it out completely.
Negligent storage issues will allow moisture to plague your motorcycle, no matter what year or brand. They're designed for all climate riding, but not endless sitting in the elements. Many bike projects on this board have spent many a year outside behind the tool shed abandoned to the vegetation. Good on you for salvaging another one.
