Failure, but I'm totally confused as to where.  

Failure, but I'm totally confused as to where.

Not sure where to begin, so sorry for the length.

So I've had my printer (MK3S) working fine for 6 months. Yes, 1st printer and learning a lot as I go (new lessons almost daily). I had a failed print happen Wednesday morning. Not the first time, but all of them including this one was explainable. Simple first layer adhesion, due to me testing (getting used to) what to do and not to do.

Once it failed, I whipped out the acetone, and cleaned the steel sheet. Then told it to print again, it did the auto home, and when it started to go down, stopped with the error message, "Calibration failed! Check the axes and run again." I then went into settings, and manually moved the X, Y and Z axes. However, I saw what I believe was some build up on Z, so cleaned off the rods, and lubed up the bearings. Got things moving freely again, and gave it another go. Went to do manual movements, and zero is at the top of the tower. Manually moved the Z to 210, and then all the way down to zero again. After this manual movements went smooth, self test passed, everything looks good. Ran the Z calibration, auto home runs, but is at the top, and the steppers hum, as it's not able to move higher, then comes up to "Please clean the nozzle for calibration. Click when done." Click the button, Z maybe moves 1 mm, and then "Calibration failed! Check the axes and run again." Manually moved it all the way down to the bottom again, and re-ran, and auto home moves it all the way to the top, and then went calibration starts again, it fails again.

Not wanting to quit yet, I tried Calibrate XYZ, auto home runs like above, "Please clean nozzle", "is the steel sheet on? yes or no". Click there, 1 mm down, and "Calibration failed! Check the axes and run again."

Basically everything is working fine, except I can't calibrate, to move on. Stuck in a loop. If I had to guess, It's almost as if, zero is not staying at the bottom, and when it tries to go down, it can't as it thinks it's zero again. Total noob, here so to me this is just a random guess to what I think is going on.

I re-flashed the board with the same version it came with (V3.8.1, Oct 24, 2019), as I've seen to many people not happy with the new release. I guess I might have  to try it anyways, but wanted to reach out first. I've also taken it all apart double checking everything slowly in the last 48 hours. (First day I was a bit upset that I couldn't figure it out and had to walk away. Thought I found some issues, and have things better now, than I did with the original assembly, but sadly, I'm still at the same point, even though I know it's put together better now than it was before when the problem started.

I feel like I'm looking at some sort of stepper failure, BUT don't know how that's possible with manual movement working fine. I'm just totally confused at this point.

Thanks in advance 

Steve