Craig, this is not a proposed answer to your problem(s) but is merely food for thought. This may all look and sound like very negative 'stuff' but in fact it is all very positive...you now know what is not causing it, so those items that you have covered so far can be eliminated from the argument. So what is left...judging by your earlier pics. all that remains is connectivity quality and the 'lower board' components. I don't have any experience of MK so it is difficult for me to comment on the actual components. I do though have many years experience of installing, servicing, fault diagnosis and finding of electronics and electro-mechanics...in that time it was established that, without any doubts whatsoever, the causes of these seemingly small and intermittent problems are to do with 1) connectivity caused by a poor interference fit, be it a single bullit connector or a flat ribbon mult-way connector...2) Components...very difficult to diagnose (unless you have available internal diagrams and diagnostic tools) meaning that the only diagnostic route is an expensive, and not always successful, replacement of parts...3) Operator (pilot) error...but unless you are doing something obviously avant-garde don't explore that path yet. I am sorry that we have not yet found the answer to your problem(s) but I will continue to think on it and get back to you if something brilliant comes of it.