Bike has just been retuned and there was a lot more changes required than we thought. So now it runs the way it always should have and I can focus on cornering without worrying about the stuttering throughout the corner.
We checked the reading of the vacuum on the ECU and they are equal. I'm not sure what the actual voltage drop was, but the bike wanted to dump a lot more fuel in the vertical.
The test was extremely easy and cleaning was a few squirts if contact cleaner, a scrub with a bristle type tooth glosser/pick and then a couple more squirts. Zero cost, but apparently something dealers don't check.