I think the 1939 and 40 Fords use the same E-brake use the same E-brake set up. I am not sure what you mean when you say," just after where the wishbone connects, it runs thru a box, and the cable is hanging up on something inside." Please post a photo of the cable running thru " the box". The E-cable does run thru the grommet in the firewall along side the speedo cable. In the 3rd photo you can see the firewall grommet and the E-cable where it connects to the E-brake handle and adjustable clevis. Below are some photos that may help.