Ok, so knowing the intended usage of the car is helpful. Just bear in mind that the soft rubber lower engine mount bushings cause extreme to/fro engine movement which accelerates the failure of the low pressure fuel line, due to binding/kinking.
I would put the values from 1.5-14.0% columns in the TB Airflow map back to stock values (leave 0.0 as .7) and see if that helps. Currently, for example, the 14.0 column is set to assume ~10% more compressor flow, which is not accurate as the turbo is stock. Leave the Desired Throttle map as how I modified it and test further.
As far as the upsized TB upgrade, your call. They would not be able to tell unless they removed the cold pipe and TB, then measured the TB with a caliper.