You mention running "open loop" appears to be OK. This would suggest to me that basically the system is sound (i.e. no air leaks, lack of compression, etc) and the ECU is responding/operating on delivered sensor information and/or out of adjustment values.
I'll hold my hand up very high and say that what I've posted is probably no different or an enhancement on what you have already concluded but is still a little confirmation of your/our current think.
MES is able to graph all "measurement" values. So one could go back to real basics and graph some values. Engine power is basically dictated by fuel delivery, air intake, temperature and other similar factors. Take a look at the list of parameters that
MES has to offer and rule out immediate "not relevant" ones (A/C Compressor, Odometer, Universal Code, etc.
Sorry not an ideal response but hopefully an encouraging one?