Here's a useless reply --- I don't know what a "MSD two step or Wot Box" is! However, if you get a manic tune, you should also invest in their switch box --- to allow all three custom maps plus a base map of your choice. My base map is a custom map from Alta's AccessPort, and the AP still functions for everything else, just not for map storage.
When you say "a non tuned ECU caused it to throw misfiring codes and put it into limp mode" --- I've always thought a Manic tune was considered to be a "custom tune" for the ECU. Have you asked your local Manic tuner if your MSD two step or Wot Box will work correctly after a Manic install?
