I was using BigBlueMenu and was able to install one of my backups but when installing the second backup .cia with bigbluemenu I started to get problems (freezing in bigbluemenu, unable to uninstall .cia or run the installed one), so I reverted back to my bakcup nand and am currently on 4.5.0-9u with no cfw installed and no emunand.
I have yet to install the Ninjhax explot on the the n3ds.
If anyone could point me out some things it would be great, thanks!
You can't run "backups" on the n3ds without a gateway/sky*
As far as the 4.x CFW for the original 3ds, you might consider trying FBI and seeing if it works any better. That CFW is unstable though so it might be that nothing works too well.
* The only exceptions are the "signed" cias, for -U consoles they include:
Pokemon Alpha Sapphire - File size : 1.77 Go, Credits to miron for the ticket and Hundshamer for the CIA file
Pokemon Omega Ruby - File size : 1.77 Go, Credits to bbmax
Pokemon X - File size : 1.68 Go, Credits to ddshoko
Pokemon Y - File size : 1.68 Go, Credits to damysteryman
Animal Crossing New Leaf - File size : 739.7 Mo, Credits to 87agyisbhdk
Fire Emblem Awakening - File size : 1.05 Go, Credits to Jefffisher
Luigi's Mansion 2 - File size : 842.8 Mo, Credits to Jefffisher
Mario Kart 7 - File size : 634.3 Mo, Credits to Pyorin (Update 1.1 is preinstalled, so you can play online right away.)
Mario & Luigi Dream Team - File size : 824.0 Mo, Credits to Anonymous (OP: 87agyisbhdk)
Monster Hunter 4 Ultimate - File size : 2.54 Go, Credits to Jefffisher
New Super Mario Bros. 2 Gold Edition - File size : 340.9 Mo, Credits to Pyorin('s sister)
Super Mario 3D Land - File size : 389.4 Mo, Credits to Ryulejzzu