Looking for a Working Save Manager to Backup Everything...

JKSM tends to work best but since it is the homebrew browser version it is less reliable then the .cia version. Some games I just had to try about 10 times to not get a solid red screen. You can try to download a new boot.3dsx from the starter.zip homebrew browser site. Also opening one of those ftp homebrew then exiting it before loading JKSM seems to improve the chances of a successful load of the game. I also like to hold the L button when the screen color changes but I think that's just an odd habit of mine lol.

 

You can copy the save data using FBI (atleast if you injected it into your custom firmware).

 

Well, depending on the firmware and which games, that might not be possible. Exploit games in particular have PASLR on recent firmware versions meaning homebrew cannot access the saves, doesn't matter which save manager you use. Not to mention most games that come out from now on will have it too.

 

Since they are going to do DSi downgrade it doesn't sound like they have cfw yet. If they do then FBI or JKSM cia file would work great.