Printer will only move up not down

New to 3dPrinting, couldn’t really find this specific issue out there.

Printer has been working good for months, lots of great prints! I received my first blob of doom a couple of weeks ago and I actually bought a new extruder motor and hotend setup from amazon (not knowing that I could clean it). The new parts installed just fine and I was able to print something after the replacement. A couple days or so later I got another blob of doom on my extruder, but this time I looked into cleaning it off. During the clean I moved my z axis all the way to the top using the Prepare->Move Axis functions, and cleaned it successfully. After I was done cleaning I couldn’t see any way to move the extruder down the z axis using the same procedure as Move Axis, so I had to manually move it down by spinning the coupler and it will not zero to home anymore and it only moves up not down.

I’ve even tried resetting everything to default so I could run bed leveling again, but every first time I run Auto Z Leveling the gantry moves all the way up to the top and stays there.

Things I’ve tried:
Partial Reassembly (tried to reseed the connections)
Resetting defaults
Adjusting tension on the couplers
Firmware update

z probe is working fine.

I always just tell it to Auto Home and that does the trick.

Yes - Auto Home here, too.

If the Z axis is moved up and the axis was set to 0 (power cycled?), it will not go much below 0 - Only up.

When homing the axis, the axis limits are ignored in order to find out where it is at.