That nut for the eccentric might be a replacement for the original. Is it possible that there was a shouldered nut or screw at one time? Are the eccentric holes a little sloppy on the bolt?
Well even if that is the original construction, a shouldered bolt would solve the problem, and you could make one with the existing bolt. Simply find a piece of brass tubing with an ID the same (actually a couple 1000ths inch bigger) as the OD of the bolt shaft. Cut a length just a few thousandths longer than the thickness of the eccentric rod. Slide it over the bolt and then install the bolt. You should be able to tighten the bolt down while the eccentric rod rides on the piece of brass tube. some guys solder the piece of tube to the bolt, some don't.
Now if it originally had a shouldered bolt, the tube should fit the hole. If not, you may need to bore out the hole a little if there is enough material.
A friend of mine made shouldered scews and bolts like this for many of his HO locos which are much tinier and fiddlier.
