Oh ok so insert the card with b9s into the actual 3ds, and the micro sd card in the ntrboot flashcart is only needed for the kit to function, and shouldnt be tampered with? im curious because on modchipsdirect website the official instructions say that to change step 3, and insert into the flashcart, and not the 3ds.
It doesn't matter what sd you put into the ntrboot card. It can be fat32 or not. It can have files or not.
I have this kit and did a little review on it:
https://gbatemp.net/threads/mini-review-r4i-kit-b9s-dual-card-ntrboot.491026/
So I know this is how to do it.
1. Put a microSD into the grey card. Put it into the 3ds.
2. Place the following files onto the 3ds SD card.
boot9strap/boot9strap.firm
boot9strap/boot9strap.firm.sha
boot.firm (this is safeB9Sinstaller.firm renamed to boot.firm)
3. Turn the 3ds on and place the magnet around the ABXY buttons such that the 3ds goes to sleep and stays asleep. Turn 3ds off.
4. Without moving the magnet, hold down START, SELECT, and X. THEN press power and continue holding all buttons for 3 seconds.
5. By now you should be in safeB9Sinstaller and just follow its directions.
6. After B9S is intalled, get luma3ds and put the boot.firm on the SD card.
7. Continue with getting all the files set up. The guide is good for that - don't want to be up all night reinventing the wheel
