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.
- The wire from IGN 2 has come off or has been cut from the coil side of the ballast during header install.
- 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.