Ah,damn.So it locks even with it set as a .nds.
Kind of, I should have phrased that differently; but It's a lot more complicated. I'll try to simplify this as much as possible: What it does is essentially block access to that specific firmware (the stock firmware) if the date is two years past the date on the card. Since it is part of the firmware, it will cause issues even as a .nds file. However, you can bypass this by setting the date back; but, it's very inconvenient. Which is why we use YSMenu, it bypasses the date lock and allows us to use our cards as long as possible. However, it has issues with certain games on some cards (r4isdhc.com cards are one of them); meaning, we are stuck using the stock firmware (either as primary, or a .nds) if we want to play these games.
Now, you said you want to use it as a .nds file. The only issue with that is how buggy the firmware gets when you run it as a .nds file. It will start throwing up errors when trying to play these games, unless you set it up correctly; but even then, it may still throw up errors after a while; and the only way to fix these errors is to reformat the card. During my own experience, I completely gave up on trying to play these games because of all the issues I was having. Frankly, it was only Pokemon Black and Black 2; and I find these games kind of boring... However, if you want to use the firmware as a .nds file; here are the steps:
1. Back up, and Format the card to the specs listed in the OP
2. Set up the stock firmware (do not install YSMenu yet)
3. Change some settings, and choose a random theme
4. Test it out
5. Boot Moonshell (if you want to use it in YSMenu)
6. Go back to your computer, and rename R4.dat to R4.nds
7. Set up YSMenu, and set it up as the Primary boot
8. Change YSMenu settings to your liking
9. Test out YSMenu
10. Test out running R4.nds, it should boot directly to the Game Screen (set the date back before-hand if you already have the soft-brick)
11. Test out a game that doesn't work on YSMenu; if you get no errors, then good job! However, if you got an errcode (usually -4 or -5), then format and start over. It sometimes takes luck to get it to work...