Well I've tried fitting a MS to a transplanted Focus RS engine in parallel with an early EEC-V (necessary to keep security, dash, better idle control, etc) and after 3 months its still not running right. As I've not got it fixed yet, I can't be certain of the problem, but everything seems to indicate poor noise rejection on the crank sensor input.
Backing up my current diagnosis is a post by one of THE megasquirt gurus who advised someone putting MS on a silvertop Zetec engine to not use direct CPS and coilpack on a V3.xx but to retain the EDIS for its better rejection.
I hope I'm wrong, but unless someone can tell us how to run MS with an EEC-V I think the well trodden path of one of the 'commercial' ECU (Omex has a good record for this on RS and other Focus) is the way.
Martin