All the pins not listed as being for eMMC and HDMI are free to use. Of course, you can use them as well, assuming you can modify your code to support that.
Yes, the boot pins are also shared by the HDMI pins. This is all described in the System Reference Manual. http://circuitco.com/support/index.php?title=BeagleBoneBlack#Hardware_Files
There is this link on the card that came in the box. If you still have it, go to the link and you will find some useful information. BOMS, schematics, System Reference Manuals, etc.
If not, here is the link http://circuitco.com/support/BeagleBoneBlack
Gerald