How should I properly ground a separate building?
Congratulations, you've created an open (floating) neutral.


  "I omitted the neutral and ground from the main panel... I hammered a new ground rod and bonded the ground and neutral at the new building sub panel, which I figured would give me the same setup as a main panel..."


This is partially incorrect. The main panel should be supplied from the utility with two ungrounded (hot) conductors, and one grounded (neutral) conductor.  You'll then have an on-site grounding electrode (ground rod, etc.), which the equipment grounding conductor and grounded (neutral) conductors will be bonded to.  

To feed your subpanel you'll have to provide at least two ungrounded (hot) conductors, and a grounded (neutral) conductor from the main panel.  Since this is a separate building, you are correct that a separate grounding electrode is required. However, you'll want to make sure it is an adequate ground before using it.  It's not likely you'll have the equipment to do this, so you'll probably have to call somebody in to verify a good ground.

If there are no other bonded metallic paths between the buildings (water pipe, gas pipe, coaxial cable, etc.) then you're allowed to simply run two ungrounded (hot) conductors and one grounded (neutral) conductor.  In this situation, the grounded (neutral) conductor should be bonded to the grounding electrode at the subpanel.

If there are other bonded metallic paths between the buildings then you should run two ungrounded (hot), one grounded (neutral), and one grounding conductor. In this case, the grounded (neutral) conductor will not be bonded to the grounding electrode at the subpanel.

See: National Electrical Code 2011 250.32(B)(1)