You can just leave the two original ballast wires hanging, no need to connect them. I ended up using mine to trigger firing my msd. One of the ballast wires is hot in 'start' other is hot in 'run'.
If you are going to remove the ballast resistor you need to put a jumper between the two connectors or you will wind up with power to turn it on only in the "start" or only in the "run" position in either case your engine will not start or won't stay running.
MSD provides a pigtail wire in the kit just for jumping those together with the third connections for the small red wire from the MSD.