I'm not sure what the problem was.
The following is the procedure I used to install my GW on the New3DS 9.0.0-20U:
1- Using OOT / GW 3.1.1, I backed up my original nand and copied the contents of the microSD cart to my PC.
2- I then created an emunand on a 64GB microSDXC, which had been formatted to FAT32. F/W on both sysnand and emunand were at 9.0.0-20U at this point.
3- I then noticed that the nice 3D video demo had disappeared from the Homescreen of both nands as a result of the GW creating the emunand on the cart.
4- I proceeded to delete the contents of the cart (IE: the "Nintendo 3DS" folder), and copy back the original folder that had come with the unit. I also copied back the GW 3.1.1 launcher.dat.
This made my emunand exactly like it was on the original nand before I created the emunand (with the 3D demo intact). But the sysnand still had lost the 3D demo. No big deal.
5- I now proceeded to unlink the emunand folder from the sysnand folder:
I did this by turning off the New3DS, removing the GW cart and microSD from the console, booting into the sysnand, formating it, and setting it like it was before, while all this time keeping the microSD card OUT of the unit.
I turned off the unit, put the microSD back into it and turned it back on. It created a folder for the sysnand separate from that of the emunand, just like I wanted.
6- I installed a few cia's, copying the savegames from the cia's on my Old3DS using SaveDataFiler. That worked very well.
So that's basically what I did before I decided to update the emunand to 9.5