First, awesome build and amazing description of the entire process! I'm been pseudo-stalking this build as I began designing and building my own arcade. I'll likely document as well, and I'll send a link Chance to make sure you get credit for all of the help -- your ideas and implementation were a great inspiration.
With regards to the ultimate i/o's, I contacted Andy at Ultimarc and he stated that he did not build in unique ID's for those boards, so it is unlikely that your OS would handle both. For the mega board setup as in this build and what I'm doing, he suggested two PacLED64s to control lights and two Mini-Pacs for controls. His trackball setup has usb options as well, but they make a mini-Pac that can handle a trackball and a spinner. I'm not sure if anyone else had success with two ultimate i/o's, but I trust Andy's advice. Good luck, and thanks again Chance!