Okay, I went a head and made an App that swaps the folder on boot, here is how that works:
On first boot it will attempt to swap the SD Cards and will say it completed, but you will need to reboot because it will end up marking the external SD card as both internal and external, after the second boot it will work fine.
Don't want to swap the SD Cards? Just disable the SDCard Swapper Fx3 app in the settings and reboot, then BAM no more sd card swap. (Or use a root app uninstaller to remove it.)
Version 10 is coming my friends.