Will this work?

Actually with an MSD (conversion) it doesn't matter if you leave the ballast in or not. Since you are not using it, I would not use it. But just for info, let's say you are converting a stock Mopar vehicle. The ballast normally lowers voltage to the coil. This would imply reduced voltage to operate the MSD. But the 'small red' connection to the original switched "run" circuit DOES NOT operate the MSD. It is merely a "power trigger on" similar to a relay. The main power to operate the MSD comes from the 'big red' to the MSD