So with further testing, I am back to losing steps on z-axis like I was once in the past. Messed with pulse length, sherline mode, acceleration, ipm and kernal speeds. Nothing seems to help. This loss of steps only appears to happen on the z-axis, x-y do not appear to be showing the same behavior.
I have been testing the z-axis with 1inch long moves and .1 inch moves. They all appear to have the problem. no matter what speed I run them at.