I get to answer my own question. w00t! Turns out two tower axis endstops were not matched up properly. It was very strange because when I did endpoint tests with m119 I was getting the "correct" values which seemed to be on the correct axis. The revelation came when when I decided to run a G28 home and manually trigger the endstops before the carriages reached the top (so I could easily see which ones stopped when). It became very obvious that the carriage that stopped was not the endpoint that was triggered. I swapped two towers and the system starting homing properly. What an ordeal of frustration for something as simple as a mis-wire! Hope this helps someone else.

As a side note, I switched back to repetier. I liked it's screen interface better anyway, and read several posts that indicated it handled "out of square" issues better, which I suspect I may run into as I continue.

Still haven't printed anything though, because I'm now faced with extruder jamming problems.