hmm, two things :
you can update to d2x v8 without problem, don't be scared about it.
v6 is now old, and some game works only starting from v7 (lot of games using wiimotion+, and older ones like metroid prime trilogy, ssx, sam&max, etc.)
you don't need to update to v10 (beta), just go with v8 final, which is the one provided by modmii.
So, you can get slot249/250 from modmii if you want then use a wad manager, or use a d2x installer homebrew and update the slots directly from the console. (if you don't know how to do, you can ask)
N64 VC are known to having compatibility issue with emuNAND cIOS mode.
a lot of N64 VC need a EmuNAND Neek mode instead.
if you want more information about emuNAND cIOS/neek mode :
https://gbatemp.net/posts/6592730
you can also check the cIOS compatibility :
http://wiki.gbatemp.net/wiki/Wii_cIOS_EmuNAND_Compatibility_List
Some games work only on specific cIOS version or base.
USBLoader should be good at making NAND dump, but it might differ based on the IOS you are using when doing the dump.
IOS58 and cIOS are using different naming method for FAT32.
I think Xflak just suggest that you make a new NAND from modmii because yours might be bad/corrupted, it's not related to the way you did it.
you can try to make a new dump from a loader, or another FSdumper too.
I'd recommend you make the dump using d2x v8 if you plan to launch channels in cIOS mode (as they will also use d2x v8's filename decoding while playing).
making the dump using the IOS you'll use is better.
If you plan to use neek, maybe using IOS58 is better than cIOS. modmii is good for neek too.