When you set up the values for the Custom Tool component, did you choose the same values as on the robot, or choose values that seemed to look right?
My guess is that your tool was calibrated with another tool axis in mind - KUKA|prc has got a slightly strange standard there that can be confusing, we are aware of that...
From looking at your screenshot I would expect the tool to be something like 0,0,300,0,-90,0 in KUKA|prc
But no matter what tool axis is used, if you enter the same values on the physical and simulated robot, the movement should be identical. The tool axis only defines how the Grasshopper plane is interpreted, it does not change the internal robot logic and you do not need to "change a toolaxis" in the code or so.
I would recommend:
Check if the values are identical.
If not, choose a set of values and go with that one - you will then either have to change the physical robot's ABC values via "Numeric Input" on the smartPad, or alternatively you need to setup your planes in Grasshopper differently. Most likely Deconstruct Plan followed by a Construct Plane where you use Z for X and Y for Y should do the trick.
Please let me know if that solves it. If you are really getting a different simulation with identical XYZABC values for tool and base, please send me the file!