Quote Originally Posted by augerpro View Post
I believe the firmware we loaded was Marlin1_0_2_Pegasus12.ino. Just manually moving the Z axis just now and it shows a position of 220 while it is actually about half way to the top. So it does appear to be going half distance, both steppers obviously since if they were different they would ind quickly. So what do you think?

BTW what does the FR 100% on the Marlin screen mean?

So when we leveled the bed with the 9 point method we used paper as the shim. So you are saying we need to adjust the Z offset in the slicer to do what exactly? Get to exact 0? Or actually move it up to whatever works well for a first layer?
Real talk, once you level your bed, you should not be using a Z-Offset. The first layer of the print should be above the bed by a very small amount. For example, I use a feeler gauge with a thickness of 0.1mm. This position will read as 0 on the z-height. It is a little weird as it truly isn't at 0mm.

This small manual offset must exist when printing, do not print with your nozzle at the print bed. Doing, this creates back pressure and your extruder will begin to skip steps. You need that small amount of space so the filament can flow from the nozzle to the bed.

The issue with your Z-Axis height is with the DRV8825 driver you see on the very top. That driver turns the motor at 1/32th of a step compared to the A4982 which runs at 1/16th. So your observation that the Z axis is only moving half the distance is 100% spot on.. To change this you can use a different driver, or change the e-steps in your firmware to 8000.