[beagleboard] Exactly what PIOs are enterally free for the user without removing functions to the BBB?

They are described in the System Reference Manual. http://circuitco.com/support/index.php?title=BeagleBoneBlack#Hardware_Files

The are also described in the Getting Started Section. http://beagleboard.org/Getting%20Started

They are the LCD pins and the eMMC. The Ethernet does not connect to the expansion headers. Neither does the USB.

Oh, you can also read the schematic. http://circuitco.com/support/index.php?title=BeagleBoneBlack#Hardware_Files