AM8 / MKS gen1.4 / TMC2208 stepper motor problems

Apologies in advance for a lengthy post. I am fairly new to 3d printing.

I recently converted my Anet A8 to the AM8, running only 1 z motor with a timing belt at the top of the frame.

Shortly after upgrading it would run a priming line at the front, but then started printing at the front where it stopped priming at instead of moving to the center. No settings had changed to cause this, it started after a manual bed level. I could find virtually no information on this, troubleshooting steps that helped, or even trying to reflash the firmware, and figured there was something wrong with my board, even though it would auto home, manual bed level, and moving the axis through the LCD with no issues.

So I upgraded to the MKS gen 1.4 controller board, 5 TMC2208's, and a Kingprint 12864 LCD.

I upgraded to the most recent version of Marlin using this guide.

Following this guide @9:12, I set my driver voltages to X/Y=0.9v, Z=1.2v, and E=1.1v.

Now when I auto home through the LCD, the z axis raises up approx 2mm, the x axis moves approx 2mm to the left, the y axis moves forward approx 2mm, then the z axis moves up 2mm again. I am not able to move the z axis below this point once it is set. When I move the axis through the LCD, X+ moves it to the left, Y+ moves the bed forward, and Z+ move the axis up.

Also, my hotend fan does not start when I turn the printer on like it had before I upgraded boards. I have this plugged into the green FAN block listed on the board.

I have scoured everywhere I know where to look, and most of the search results that have come up. I'm honestly lost on where to start to fix this.

Edited 1 time(s). Last edit at 12/25/2018 12:46PM by Recoil1980.

Update: I went through the Marlin configuration for my Anet setup, and cross verified several settings that were not made when I did a fresh install for this new board. There are too many to list individually, but that fixed my issue with the axis movements...

My end stops were wired up wrong, and I had to wire them up to be connected to the GND and D# pins on the connectors.

The only problem I seem to be having now is with my hot end fan not coming on. I have it wired up to the green FAN connector block on the board (D9 of previous image), but it is not coming on when I turn on the machine, or when I start heating up the hot end. I have my part cooling fan plugged into the 12-24v & GND block at the bottom, but I don't know which settings I need to correct so they come on after the first layer.

With neither of those working I am not even able to tell if my extruder is going to work yet or not, but I do have some progress made.

fans have polarity, they must be plugged in the correct way around

You cant software control a fan that is plugged into 12-24v & GND, its should always be on.

I have 3 of these, or should say had, connected and verified the polarity on them (https://www.amazon.com/gp/product/B00BF3S83C/ref=oh_aui_detailpage_o04_s00?ie=UTF8&psc=1). They still were not working no matter which pins I was trying to hook up. So I took them off and tested a couple of other fans, which worked...the fans I originally was trying are no longer working for some reason.