Was running but now after pulling alternator wire, it won’t run

Just exactly which/ what wire are you talking about?

The alternator should have nothing to do with whether the engine will start and run

Check that with the key in the run position, that the MSD is getting power to the "small red." Then while watching the voltmeter, crank the engine USING THE KEY. Again the small red should be getting power

ALSO make CERTAIN the "big rid" is getting power at all times, and that the large black is grounded

There is a troubleshoot procedure over at the MSD website