The USB hub & Audio work flawlessly and have fantastic sound quality. Really impressed.
Still waiting on the wi-fi modules from China and I've been let down on the LCD supply again..... still struggling for a screen on this.
In the meantime I think I've solved the USB power/Host problem, leading to a single port that will charge and act as a standard USB port. I've integrated an always on 3v3 20mA supply in order to have a watchdog micro-controller in charge of the system, monitoring the battery and power switching circuit. I've got another PCB coming in to test this section of the circuit.
Here's the PCB...

It's quite small and literally does all of the above and includes over voltage protection, instant on to cope with a totally discharged battery and 1.2A charging.
Status so far:
Power Regulation - CM3 supplies done
CM3 working fine - booting retropie
18 & 24 bit DPI working perfectly
USB - 4 ports available to CM3
Audio - Working perfectly to speakers & headphones with auto speaker cut off, analog volume control working.
In progress:
Battery Charger/Host USB-OTG Power/LDO Power - Design complete - Boards in Production & Components Ordered
To do:
Finalise Safe shutdown - waiting on new charger/power board.
PWM Dimming of LCD Backlight - still toying with inclusion of Arduinio and consolidating watchdog/controls/dimming/other all in one place.