I've seen people levelling their Z axis by measuring from the bed, but this doesn't seem like a good idea, seeing as the bed is a moveable object. I think it's smarter to level the Z axis by measuring from the frame.

This simple object is a post that fits into the space between the bed and the towers. You hang a dial indicator from the X axis rods and put this post underneath it. Measure the height under the X stepper motor side, then go to the idler side and make it match up.

Print this as it appears in the STL. When it's finished, scrape the top smooth with a knife. The smooth side that was in contact with the bed is the side that you present to the dial indicator.