have your tuner turn off the CELs for p0301-4 if you no longer wish to see them from the light weight flywheel.
Do the boost leak test, then report back. You can install pinks into a stock ECU car and it will idle just fine (stable). Since you report it is rough then I'm guessing the turbo inlet is torn, or there is an air leak some where in the system (boost leak test will find this). In short, the tuner would have to be an idiot to not be able to get it to idle smooth since it takes virtually no changes to do so
Change the scale size and you are set. Maybe fidget a little with the MAF table for the intake, but it should still idle smooth on those injectors.
As someone else pointed out, you will be running out of injector size depending on how aggressive the tune is done. It will be close.
The surge in the higher gears:
You need to data log and see what is going up and down. Is it boost pressure, timing advance, etc. That will explain quite a bit.