Yeah. I want to build a LR for full sheets of plywood but don’t have the space for that. Some day. Until then the Primo has been running great until upgrading the board.
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LR2 upgraded with a Jackpot I bought a couple of weeks ago and am just getting back to. I am having the same endstop issues as well. All of the endstop lights are on.
Okay. I think after all of this I made a wiring error. I took off all the wires and verified connectivity with my meter and then reconnected them as I thought I had the initial time. Now my X and Y both home properly. I think that @steved was correct in that the Y1 motor was paired with the Y2 endstop and the Y2 motor to the Y1 endstop but since I removed all the wires I will never really know for sure. I do appreciate everyone’s time and energy on this issue.
Now if the Z homing button could be removed from the web UI so I don’t send it off the core, everything would be perfect.
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We have never been able to use “Home All” on an MPCNC. I can actually change it on the Jackpot (and I will) but this is not an error this is how it is also set in Marlin.
We home X then Y, then separately probe Z.
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The button can not easily be removed, I can stop the home all button from using Z but the button will not be moving in this version.
Still it should not go off in Z when pushing the “Home Z”. It shouldn’t do anything then. 
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Not having the button on the interface makes it more Bruceproof!
Currently, I can not change that code, it is above my pay scale. V3 of the GUI is nearly ready and at that time it “might” have the option.
Sorry but there is just no reason to push the home Z button, and the amount of work to maintain not having that button is a lot more work than it sounds. Now that you now it should not be hit, what are the chance you push that button?
I can and will fix home all, which also should not be hit, but nothing I can currently do about the Z button.
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Yeah, but there will always be a bigger, “better” Bruce that will come along…
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The MPCNC config file has Z homing going positive but sets the Zmin endstop. So when your code tries to home Z, it goes up and never hits an endstop (or thinks it doesn’t since Zmin is the triggered endstop). You have to change the following lines:
motor0:
limit_neg_pin: NO_PIN
limit_pos_pin: gpio.39:low
limit_all_pin: NO_PIN
Then it homes Up and will trigger the Zmax endstop.
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I found a printable file that let me put a limit switch on one of the Burly Z bolts, so I’ve got a Z max endstop. I’m running grbl on a CNC Shield controller, so that part of the config was trivial but my experience probably won’t help most folks here running Marlin on one of the standard V1 boards.
The ability to put a switch there would help. 
This one should do the trick: Printables
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Should be in the docs then. The question is: Why can’t I home X and Y when no endstop is connected and an error is shown? With Z it does not show an error but tries to home. Isn’t that kind of weird? Should it not be configured the same, just giving an error and doing nothing?
Also: I always push all the buttons to see what happens.
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Kids… 
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Updating the yamls now. Z home does nothing, home all only does XY. Win Win.
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How do I get that on the Jackpot? I am also taking a link. I haven’t dealt with anything regarding the Jackpot yet, just slapped it together today without reading too much. 
Just download the yaml, and upload it to the board and power cycle. Done.
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It works, incredibly easy, thanks. No more accidental Z liftoff. 
Sweet!!
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