Flex PCB aside, you could just cut out the section of board with the NAND and eMMC. Nintendo provided handy dummy pads for all the data lines on the TSOP NAND, and you can grab the eMMC signals from the nearby series resistors. Either way, the NANDs are like the one thing on the mobo that should be a piece of cake.
That's exactly what i was thinking. once we get this thing booting from custom regs, i will give this a shot!