Not good, but sounds like you might be getting to the bottom of it, finally
Any other cars had similar problems or is this a one-off? Have mountune accepted responsibility for it?
MR200 is a limited kit, only about 30 odd of us and if you include all the MP165 and MP185 (and include all Focus and RS kits) there must be several hundred conversions now, none of which have this issue. I am only aware of one RS with a similar issue.
The only connection with Mountune could be that the engine management system has just had enough of the extra load, this is highly unlikely.
Mountune are aware but even they think it is a voltage issue however see what they say, Ford do think it is the engine management, potentially just one tiny circuit not working properly, cold, damp, dried out circuit.