Do the wires look ok inside of the wire loom? I have heard of a number of guys having this problem and it was from the wires melting because they were too close to the header tubes. There are a few other scenarios but since this happened after the header install I would definately rule that out first. A scope would verify proper VSS operation while driving down the road to test the sensor itself but most guys dont have equipment like this to test with. A scan tool will also show VSS as mph but is likely going to match what your speedo is doing. I would take a closer look at the harness and pull the loom off and see what the speed sensor wires look like. Also you should use an ohm meter and test between the VSS connector and the PCM connector to make sure there isnt a break in the wire. With an ohm meter hooked up on each end of the wire you can wiggle the harness and watch for an open
