Check your voltage at the battery terminal on the alt. and battery POST not cable Should be within .2-.5 V at worst.
Then check V going into the ballast at idle. Should be about the same as the battery and Alt.

You can also see if it V increases with RPM.

try a ballast. They are cheap and can cause these symptoms when getting ready to fail

Also as SCG said VERIFY the ground on the ECU. Ideally it should be grounded directly to bare metal on the ECU & motor