Harpers Ferry is USA home territory so cannot be in rail supply for CSA (7.1). However I think both Harpers Ferry and Martinsburg can be in road supply via Bunker Hill because it is south of the Potomac(9.2) and 7.1 does not forbid road supply in USA home territory. So Forks (not in mud turns), Martinsburg and Harpers Ferry could all be in CSA supply. That is how I see it with current rules. It would be nice to have a "supply map" shading all hexes that could be CSA supplied (not counting leader supply) - this would remove any ambiguities.
The CSA cannot trace supply north of the Potomac by any means. Rule 9.2 seems pretty clear about that. But it also seems the CSA could use the roads in the Valley to trace supply right up to the Potomac through Bunker Hill and Martinsburg.