To make MS work with stock ECU (piggyback style), you need to share the RPM signal, as well as other signals (coolant temp, intake temp) possibly more. For the stock ECU to fire the sparks correctly, you must trick it, so it thinks it still is controlling the fueling. This is tricky, you can't just wire MS in parallel with the ECU, i think there was a special board for that. As well you must simulate the AFM signal through one of the MS outputs or the ECU will retard the timing, and you car will run like crap.
You should read the megamanual.com, it can explain everything better than me.
My advice would be, to ditch the stock ECU, and wire everything through MS, but be prepared to spend a LOT of time making it work though...
Or you can just wait until I complete my MS II Extra project, and write a complete "How to" manual
