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?