the internal flash memory has a mmc interface onchip, it looks like:
There are chips with 32 GB! (but with BGA it gets difficult to change).
Have you thought about useing a mini-pci-e SD card adaptor?
I tried this one: MR09R
but without the proper drivers (it's connected via pci-e lanes, but it is not recognised.
Any idea how to solve? Beside the additional memory it can be used to catch the USB lines on the connector :-)
ad 2. 3G module
Are you sure about the SPI interface, I checked the module and it uses the USB lines and USB0 comes up if the modem is online. Maybe the SPI is used in combination?
ad 3. I2C Audio
There might be more functions over this interface it's connected to MC13783 Audio, USB OTG, Power Management
Can you figure out how to turn the USB OTG into master mode? Connecting with a microUSB-A adapter doesn't do anything.