Ok so the transfer process has been a complete disaster.
First things first. I realized that console region also included the country you set your profile as so that was quickly fixed and was able to move things along. I wasn't able to pick the "essentials" wireless transfer since the 4 GB SD card was still too small to receive the data, so I had to choose the "via PC option". It transferred a some system data through wireless and prompted me to manually transfer the SD files. I moved the data from the n3DS 4GB card back onto the old 64 GB card since I had a few save files I wanted to carry over, but since it offerred to overwrite some files, I only moved what wouldn't overwrite anything.
Supposedely, even though any games downloaded would need to be redownloaded, the previous save file would have been transferred over and allowed me to continue where I left off. I tried with two games I redownloaded and it had no save files. I went to Manage Data from the 3DS Settings and while it found no save files, it had all my GBA Injects greyed out and with a small cross to them.
I then tried opening my friend list since I'd assume that at least carried over and it said there were no Miis created and I had to do that first. That weirded me out bad and put the original 4 GB SD card back on and it also had no Miis or friendcode.
So I basically transferred my emunand system but now I can't access anything from the old system onto the new one. Plus I ended up having to reformat my old system.
So a few questions.
First, what exactly happened and how can I salvage at least some of my old account. On SD > Nintendo 3DS, There's 3 system folders, one with today's date which is where I think the save files from the old one should go or something.
Second, Could I technically restore my old emunand on my console? It seems to be on a clean 9.0 now. I think I
Edit: My eshop data (funds, redownloadable content) is on the system itself. So that's something I guess.
Snooping around
https://3ds.guide/move-emunand I figured this could be what may be the issue. But a few peculiarities arose and I really don't want to screw up.
On the first step regarding DSiWare, on SYSNAND TWLN -> title, instead of a folder 00030004, there was a 00030005 and 0003000f folders. (no biggie I thought and did the same copy over to 0:/gm9/out”
Then on step 4 "Move Emunand to sysnand" things weren't not compatible at all. First, there's no [E:]Emunand Virtual option but there is a [S:]Sysnand Virtual folder, which also has a nand.bin file. When I select 'NAND image options', instead of "Restore SysNAND (safe) I get "mount image to drive", "update embedded backup" and "verify file".
Since that was very different, I decided to ask here what might be the issue but it's so confusing...