I can only try to reason out the problem, as I do not have that controller.
Typically, the presetter has some parameters which describe the position of the presetter touch off point in the machine coordinate system (G53). I would attempt to adjust the X parameter of the touch off point, so that when Tool 1 (master) touches the sensor, the position of Tool 1 is diametrically correct in the G53 coordinate system.
In my mind, I do not want any X value in G54 other than X0, whereas Z can be whatever it needs to be.
If Tool 1 is set up in this manner, then its X offset will always be very near zero.
Now, when the other tools touch the presetter, they will most likely differ from T1. Whatever their difference is, should be the X offset amount for that tool.
In this manner, you won't be suffering from the complications of shifting the entire work coordinate system in X, which throws all the rest of the tools off.
I think where you are getting in a bind with your method is touching T1 off the part to set its offsets, particularly if T1 has some considerable amount entered in its X offset register. This causes you to be chasing two interdependant reference points.