I run MS2 extra (beta 9 still, not got around to updating), haven't removed motronic or run any of the gauges off megasquirt. I hear that you can though. I don't drive the pwm idle valve either, I couldn't get it to respond properly. I can control a lightbulb etc off the pwm circuit, but not our valve. I use the pwm circuitry to control a veedub aux air valve.
MS can improve response, a good AE tune is critical to this though, and difficult to master! I have a good AE tune on mine imo.
