Ignition problem

If the engine runs in the run position the ballast is fine

What the op has described is a typical no power to the bypass (IGN 2) during cranking.

It can happen in a few ways.

1. The wire from IGN 2 has come off or has been cut from the coil side of the ballast during header install.
2. The ignition switch has failed (coincidentally to the header install)

My bet is the IGN 2 wire has come off the coil side of the ballast.