Changing the home position on a Prusa i3 MK2
Consider the original installation with the orientation of the Pinda probe to the nozzle. Let's say for argument's sake that the Pinda probe is 3 mm to the right and directly in line with the nozzle on the y axis.
If you examine your new nozzle, I would expect that the relationship of the nozzle to the Pinda probe no longer matches the original spacing.
If possible, re-design the mount to place the Pinda probe in such a way as to match the original design.
Thanks for pointing out my oversight, Mac. If the relative position of the nozzle and pinda probe are as the original, the solution is then in changing the appropriate parameters in the firmware.
I found a reference for someone who had a bit smaller error in home position, but the concept is the same.
The link above points to information reading thus:

In Configuration_Prusa.h:
Code: Select all // Home position
define MANUAL_X_HOME_POS 0
define MANUAL_Y_HOME_POS -2.2
define MANUAL_Z_HOME_POS 0.15
// Travel limits after homing
define X_MAX_POS 250
define X_MIN_POS 0
define Y_MAX_POS 210
define Y_MIN_POS -2.2
define Z_MAX_POS 210
define Z_MIN_POS 0.15

it will be necessary to connect the printer via USB to a computer running an Arduino IDE and to load the Prusa specific files for that printer. Edit the noted location, save/write the configuration and test.
I would suggest small adjustments in only one or two parameters at a time, to avoid ambiguity in the cause/result sequence.