Appreciate the response Will. I did follow the assembly instructions for squaring the machine which seems to encompass bullet two. The machine itself was square after that step.
The method I was using comes from the Shapeoko Wiki: Excellent discussion of leveling an SO3 http://community.carbide3d.com/t/x-rail-not-level/7445/8:
- Level a Y rail, front to back. (Call this Y1)
- level the other y rail, front to back (call this Y2). If the world was perfect, you now only need to get the two Y rails level with each other now. It’s never that easy.
- Move the gantry all the way to the back of the machine.
- Level the gantry left and right by adjusting A back foot - for the sake of argument, the rear Y1 foot. If you adjust more than one of the back feet, you need to start over. That’s a hint. Don’t do what Donny Don’t does. Adjust one and only one foot
- Put a level on Y1, front to back, it probably isn’t level. Level it, adjusting the front foot only.
- Put the level on Y2, front to back, it should still be level, but probably isn’t (you didn’t move the back foot or front foot…). If it isn’t, adjust the front foot only.
- Move the gantry all the way forward
- check the gantry for level left to right. It probably won’t be level, but it will be closer than last time. Adjust the Y1 front foot a touch, and it should be closer. Now go to step 1…and don’t touch the rear foot on Y2, and keep cycling through all this until it’s “close enough.”
In my case, I feel that step 8 seems to be undoing step 5 or perhaps I’m making too large of an adjustment and should be moving the leveling feet in half turns.