things you should take in account:
if you want a minimal setup, I'd recommend d2x r52 base57 in slot 249 (that's all, only one cIOS to install).
r52 has more compatibility with hardware, base57 more compatibility with games.
r52 works only with USB Slot0 (bottom on Wii, back-top on WiiU)
on WiiU, you need a y-cable if your drive is not externally powered.
Like said on previous page, the problem is not the loader but the patch.
it seems the way he did the HID access is not compatible with HDD plugged at the same time.
Of course, you can launch the disc from USBLoaderGX ! it's a good idea to test the patch without a HDD plugged
you still need d2x r52 installed, launch the loader and insert the disc. instead of "install" select "mount", go to the game settings to enable hooktype, save the settings, and launch the game.
it should load gameconfig.txt and the patch should not conflict with HDD anymore.
it's a good way to confirm the problem is the patch.
the gameconfig format could be learned by reading the GeckoOS's or a loader's sources.
but it's not complicated, it's really self explanatory.
TitleID of the game (you can have multiple titleID in the same .txt file)
TitleID accept jokers (? for any letter)
poke : write value at specific address
if equal : check current value of specified address 1 with value 1 and poke address 2 with value 2 only if 1 is equal
codelist : edit the "memory range" used to put the Ocarina gct file in memory. for example here to make the memory bigger than the default location for all other games.
hooktype : well, the hooktype to force use for that game
there's another patching format you could use if you want the loader to verify current address before patching : WIP.
the WIP patching format is already a feature in USBLoaderGX, you just but your TitleID6.wip in sd:/wip/ folder, but it's just the same than using gameconfig "pokeifequal"