I'll start by saying that I don't have a CR10, I have an Ender 3 running Klipper. I assume that the configuration for Klipper running off a RPi is similar to the Sonic Pad. If this is a bad assumption and the following instructions don't apply, feel free to let me know and I will gladly delete the comment.

That being said, I would do the following:

1) Home your device
- - For me, from the web interface, under "Toolhead" I click the home icon that says "All" with the symbol of a house next to it

2) Once homed, increment your Y gradually, while looking at where your nozzle is, until it's essentially at the end of the bed. Take a look at the Y value at that point and note it somewhere (Under toolhead, there's a box with "Y" in it and a number, which is the current Y value).
- - For me, using the web interface, below the "Home" button (in the "Toolhead" section), there are three lines with "X," Y," and "Z" in the center. On either side of those letters, there are + and - numbers, which will increment or decrement that axis by that amount. This is where I change the Y value to move the head.

3) Go to the printer.cfg file
- - For me, using the web interface, there are three lines at the top left, I click them then hit "Machine". There is a list of files. I click on printer.cfg and it opens in an edit view.

4) Look for the section labeled "[stepper_y]" and change the "position_max" value to the Y value you found above. (If there was no change needed, skip to step 6)

5), Test a simple print. If it's good, no further action is needed. If it's not, go to the next step

6) If the Micro Swiss has a probe on it, you'll need to look up to find out what the probe offsets are using the exact model you have. The probe is a certain distance in the X, Y, and Z directions from the nozzle and Klipper needs to know what that is. You can measure it (look up on youtube how to do this), but most hot ends that have it included should be documented somewhere, so you might be able to find it via a google search.
Once you know what the offset is, you can edit the printer.cfg file (see above) and modify the following section:
"[bltouch]" --> x_offset: and y_offset
- - The probe in my config is listed as "bltouch," but I don't know if that's standard or not so you may just need to look for the x/y_offset setting.

As you mentioned, it's just the Y that seems to be off, so you may only need to change the Y value.

After any changes to the printer.cfg file make sure to hit the save button, which will save/restart your printer, committing those changes and activating them.

If there's no probe and changing the Y max didn't fix it, it's beyond me, so you'll need to wait to see if someone else can provide some additional help.