Lulzbot Mini out of control

I clogged the hot end of the mini with some cheap flexible filament and in an attempt to unclog it I got a toothpick stuck all the way up to the nozzle (I’m not a very smart man).
I ordered a new hot end from Lulzbot, though I know they say it’s not a direct replacement because you have to change some wires on the connector I was able to follow the directions that I found here (https://ohai.lulzbot.com/project/replacing-lulzbot-mini-hexagon-hot-end/maintenance-repairs/) and I thought it went pretty well. I mount the head back on to the Mini, feed some ABS into it and it extrudes like a champ. I decide to print a calibration cube to test it out and that’s when it all goes wrong.
During the print process the print head never moved along the Z axis so I stop the print and I try to use the controls in Cura to move it manually to no avail. I then start to test all the other controls and some work but others don’t.
I’m new to 3d printing so I didn’t know exactly what to try so here’s what I’ve done to try and troubleshoot it.
Flashed Default firmware with Cura: no change
Flashed New firmware with Cura: no change
Checked all the pins using this diagram (https://ohai.lulzbot.com/media/uploads/Wire_Diagram_1_1.png.600x0_q85.png): no change

If anyone can point me in some direction that would allow to figure this out I would greatly appreciate it.

With the print head sitting off the ends of travel on all three axis. What does the M119 gcode command entered in to the send box on the control window of Cura give back.

This will show if any of the stop switches are triggered that should not be.