Matt, are your prints still stopping early?
One other idea I thought of to check is the z-limit or end-stop switches.
At the top of each set of vertical rods, right where the belts disappear into the upper housing are three micro-switches that are triggered by the carriages when they are at full z-stop or limit.
Just using a finger, gently check the actuation of each of the three switches. You should hear and feel a small click each time it is pressed. All three should sound and feel the same.
I am just wondering if it is possible that a bad switch is being triggered by machine vibrations and that is telling the printer to stop because it has reached the limit.
You can't always tell a bad switch just by feel, but sometimes you can. It may not click, or it may be sticky, or feel soft.