They should of narrowed it down by checking if there is a live to the sensor and a return from it on start up, also reading in the correct scale amounts. Just seems strange that it works well with the standard TB but not the 60mm. To me that's a throttle body fault rather than PCM. Unless it does eventually play up with the standard one back on it
auto electrician was looking at it today (not heard anything yet), yes agreed on original TB, can only assume the mapping is looking for specific data back from the 60mm TB which it probably is sending but not reading it whereas it may be satisfied with what the 57mm TB returns. Really have no idea myself. Ford are talking to Mountune though for extra help, will keep updates comings when I hear more.
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