Hi Michael,
I'm glad you solved your problem.
My general comment. The idle is intended to be controlled by the computer, so it is good and stable hot or cold. If the software has been reflashed then it should be working as designed. That fixed my problems including the uncertain idle and high idle speed in some circumstances, and other poor drivability problems.
But it does appear that your base throttle setting was incorrect 
. It may have been set incorrectly at the factory or been incorrectly adjusted later. I forget the details now but I believe the dealer is expected to set that and the cable adjustment before doing a reflash.
Good luck Jaahn
Here is the report I posted. July 28, 2021. #4
I had the software updated on my Gran Turismo in 2020 as I wasn't happy with the way it ran. Mainly the uncertain idle and a big flat spot off the idle. The local dealer said he always did the update from new and was surprised my bike had not been done by the previous dealer and said calibrating the idle throttle adjustment was also important.
I was very pleased with the running after the upgrade and it ran much better all through the range. The idle is certain and the flat spot is gone. I am very pleased with it. 
Not perfect for ordinary city riding but very improved and much more fun to ride.
I had trouble with the battery struggling to start when I used it as I do not ride very often. I needed to jump start it most times for the first start. I fitted a lithium battery and the problem is solved as it holds the charge OK between rides. :love: