Actually.. it worked. I renamed the old bootmi and sneek folders for backup, and put the freshly created from ModMii on the SD and could boot into the emuNANd using USBLoaderGX and also by using the channel.
Effectively the SNEEK installtion and the emunand now ARE exactly the same as DURING all the previous tries. The only difference is that there's a lot of other stuff on the drive, too, from my old USB-Setup. So there must be some unknown dependency..
I had to replace the emuNAND, though, because the old emuNAND already is partially broken and doesn't create savegames for some games, like 2fast4gnomz for example.
Some games not being able to save anymore in emuNAND is one of the reasons why I wanted to move away from USB, because I hope it will work more reliably with the internal sd card.
Also I had to use pure SNEEK. SNEEK+DI won't work. I don't want to load WII-Games from storage, but I would like to be able to access the Neek2O menu for configuring emuNAND path to another one, though..
I think di is needed for the Neek2O configuration menu 2 work, isn't it?
So I now have a clean emuNAND and it's booting from the SD card.
I will now integrate all WiiWare into the emuNAND and hope it will keep working.
Thank you so much!