That picture you reverenced is for the MPCNC, not the lowrider.
The Primo has 2 X motors, 2 Y motors, and 1 Z motor. The LR2 has 1 X motor, 2 Y motors, and 2 Z motors, so the wiring would need to be different. I actually question how you’ve got these things wired according to that diagram when the number of motors for X and Z is different. It seems to me that you might have the function of each of these motors different.
I haven’t looked at the LR2 specific firmware, but looking at the parts list for the LR2, I do not see microswitches listed. I don’t see provisions for endstops on the parts, but haven’t looked really close.
Keeping the machine level with Z endstops might work, however, since the machine does not have an absolute zero, unlike a 3D printer, this could be tricky. Maybe having optical endstops at an arbitrary height would work, provided that they didn’t get chips/dust in them, or were cleaned out prior to any attempt at homing. In any case, the firmware would need to be adjusted from the version for the MPCNC.
To use the dual endstop firmware (In order to get dual Y endstops on the LR2) I would wire the board as follows:
X goes to the X driver. Simple enough. The E0 driver for X2 would be left unused. I would probably just wire the X endstop in parallel to both X_Min and X_Max so that the firmware didn’t freak out when X2 doesn’t home.
Y1 goes to the Y driver, Y1 endstop to the Y_Min endstop connector.
Y2 goes to the E1 driver, Y2 endstop to the Y_Max endstop connector
Z1 and Z2 wired in series to the Z driver. Touch plate wired to the Z_Min endstop.
This won’t level the gantry for homing Z, but you will get the expected results when trying to home Z. It will square the Y axis to dual endstops.
I don’t think that the LR2 was designed for use with endstops, other than perhaps the Z touch plate.
Given what you’ve described for the movement, I would surmise that the X and Y (on the RAMPS) are connected to the 2 motors on the belts on each side plate. This would have the effect of X jogging one side, and Y jogging the other. Z1 is connected to Z, but Z2 is connected to something else. Not sure what, since you haven’t mentioned it connected to anything else, and you have not described X moving at all.
It would be worthwhile to use M119 from a terminal to query the endstop states, which might give you some more insight into what’s going on.