Yep, running M800 here and no dramas like you are having. And yes the motec runs the injectors - I don't even understand why you would keep the stock ECU to run the injectors - doesn't that defeat the purpose??
Sorry I can't help you with your ignition issue, but on the point of Motec running ITB's, yes indeed you can. As Doo-Doo pointed out, tune it all up on TP, then do a secondary load map based on MAP.
Have you tried asking the question on the Motec forum in case they can help?