What method did you use to attempt to remove your vWii mods? Also did you ever install any CIO's at all (for use with usb loaders etc)? If so this could actually be the reason for your update woes. I've had this happen to me before and I've seen others complain about the same thing here on GBAtemp. If you ever installed any CIO's that happened to become corrupted (or you accidentally installed one or more that were designed for the physical wii console, as opposed to the vWii), this can cause an issue updating.
I honestly don't know why as the vWii is completely seperate from WiiU mode, but i'm not the only one who's had these issues updating. It happened to me when i first went to softmod my vWii, I accidentally installed outdated CIO's (intended for use with an actual wii), and i had to use the same installer to uninstall each one. I believe i had some corruption issues as well, but from that point on it was fine. I uninstalled them and then reinstalled the appropriate ones for the vWii and the updates worked fine again.
As for your freezing and other issues, i'm not sure. But hopefully, you can get the official update to run, and this "should" take care of the issues you're having. To me personally, it sounds like a software issue. Once you get the official update on there, it should eradicate the update you have on there now (which sounds like it may be corrupted or something).
If the CIOS method I mentioned above doesn't apply to your situation, I suggest, unplugging the WiiU (again) and just leaving it unplugged over night (overkill, but hey why not, can't be too careful
) so it clears out completely (RAM etc). Normally to clear out the RAM only takes 3-5 minutes without power (technically), but if you're going to be sleeping anyways, why not? lol, its not like you're going to be using it
. Then plug it back in and try updating again.
If none of the above works, you could try using the format option in the system settings, however this will NOT remove any CIOS's or other firmware mods you've done to your vWii. However it will wipe out ANY and ALL other channels and software and save you have on your console (both Wii U mode and vWii mode). While the eshop etc lets you redownload what you've purchased at no extra charge, there's no way of knowing if you'll even be able to get back into the eshop etc to redownload it.
I suggest only using the format option as a last resort for this very reason!