Port0: vWii HDD (partition 1: FAT32, partition 2: NTFS)
Port1: WiiU HDD (formatted for Wii U use
Both drives use a Y cable that is drawing power from an external USB hub behind the console.
Port2: Wii U GCN Adapter (only connection, not the rumble wire, rumble wire is plugged into external USB hub behind console)
Port3: empty
This works fine with WiiFlow Lite. It picks up Port0 (USB1, part 1) for the GCN games and Port0 again (USB2, part 2) for the Wii games.
For Nintendont, from what I am understanding of how it works, it is doing this:
#Mount#
Port3 = empty
(skip)
Port2 = not an HDD
(skip)
Port1 (Wii U HDD detected, attempt to use, error out)
And it will never get to Port0.
However I seem to have found a solution to this problem by starting Nintendont's application first via the HBC, and then exit. It picks up on the drive correctly if started this way. So it seems that it is only improperly loaded when called to from an external loader. It's not a massive problem as I don't have any real GCN games that I want to play currently, and most that I do play will be on my actual GCN.
If you take any requests for WiiFlow Lite, might I ask for a "Return to" destination to the Wii U Menu (if using Wii U)? There is already a channel on vWii that lets you boot into it, but it seem to hang when used.