I'm familiar with 9mm and 3/8" axles, but I've never heard of them having issues with fork clearance. Are you positive that everything is lined up? I only ask because I've done that before. And by that I mean far too often. 700 Wheel is likely on to the cause.

Depending on how your hub is constructed, the axle COULD be replaceable. You would have to essentially rebuild the hub's internals, or replace the bearings if you did so. Wheels Manufacturing makes a multitude of replacement axles.