the only thing i can say, and im no pro mechanic, is Drive train(Automatic or Manual) has no bearing on the ECU... the ECU is the Eletronic Control Unit. it is what controls your fuel-air mixture for combustion. i could be wrong though.
Hi there. Not wanting to direct people elsewhere but I'm a member of the 323f.com site over here. Very active site with so many guides and a few members who have done or are doing the ze conversion. If you get really stuck pop in and have a browse.