I've read this excellent post by Some Hardware Guy, and I'm aiming toward something similar to what OP was doing which is a Beagleboard derivative.
I've done some more research and it seems that experienced board designers advise the use of professional tools for Beagleboard-type high speed designs, like Altium or Allegro. Are there any very specific reasons why one could not use a tool like KiCad for high speed designs? Are the free tools missing the required signal integrity simulators, or are they simply too much trouble given the complexity of the job?
I am also a software person. Though it sounds like I'm more experienced with hardware design, I haven't yet done a board this complex. So I'm trying to evaluate if these free tools are useful as long as you really know what you're doing, or if I should not even bother until I can afford a professional tool (and learn it).