I was solving now similar problem. After updating to 1.03 firmware, udoo stopped booting from eMMC and it was possible to boot only by manually...
If you need always on fan, why not just connecting it to CN12, pin15? No need for special connector..
seems as PCIe 2x:
01:00.0 SATA controller: Marvell Technology Group Ltd. Device 9215 (rev 11) (prog-if 01 [AHCI 1.0])
just confirmed that this 4 ports SATA adapter is working with Udoo :)
Nice step by step manual is for example on https://www.ubuntu.com/download/desktop/create-a-usb-stick-on-windows
I used it to install Arch.
I have found small SATA adapter with 4 ports directly to M.2 - link
But I would wait till someone really tries it :)
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