Sure its kind of a mess though.
Ok, so here is what we are going to do. Its a bit of a slash a burn, but at this point I wanna see if we can get a working system at all, and then we can start trying to narrow down the problem.
I assume you have a backup of the contents of the sd card already? If not go ahead and make one. Simply copy all of the files and folders to a folder on your PC.
Once that is done, delete everything EXCEPT the following folders/files:
/3DS/
/luma/
/Nintendo 3DS/
/updates/
00040000000EDf00.sav
menuhax_imagedisplay.bin
menuhax_padcgf.bin
ropbinpayload_menuhax_USA12288_old3ds.bin
slot0x25KeyX.bin
Inside the /3DS/ folder, delete the following folders if they exist:
/decrypt9wip/
/emunand9
/luma3ds/
/rxtools/
From the updated releases of Decrypt9WIP and Emunand9 that I had you download earlier, copy the /3ds/ folders to the sd card, overwriting/merging if prompted. Do not copy any other files, JUST the /3ds/ folder and its contents.
Download the following files:
Luma3DSv5.5.7z
starter.zip
From the Luma3DS archive, copy the /3ds/ folder and Luma3DS.dat to the sd card and overwrite/merge when prompted. Do not copy any other files/folders EXCEPT Luma3DS.day, /3ds/ and its contents.
From starter.zip, copy the boot.3dsx file to the root of your sd card. Do not copy any other files or folders except boot.3dsx.
Now attempt to boot the console. It SHOULD launch menuhax and load straight into the homebrew menu. If it does, try to load decrypt9 or emunand9 from there. It may take two or three tries/reboots to actually launch the program(s).