I redesigned the board in Eagle - I'll upload the SCH/BRD files once I've tidied them up, just bear in mind it's still very much a work in progress.

Note the following: 

• footprints for all the original hardware (controller ports, power and reset buttons) 
• power input headers at the top left - inputs for all voltages are included to allow for testing without installing the power regulator (just left of centre)
• USB hub circuit to the left side of the board - left as headers to give some flexibility in where to run the USB ports to (most likely under the cartridge flap)
• headers for connection to SD card breakout board - the regular compute module with  eMMC can be used without this but needed for the compute module lite.  Again, undecided on where to physically run the SD card socket to but hiding under the memory expansion cover is a likely candidate, hence where the headers are.
• Full sized HDMI port used (top, just right of centre) mostly for convenience when testing (and I have a stock of them left over from a previous project).  I'll use a short extension to bring this out to natural N64 AV port.