I've been troubleshooting this as well. I've been using your HackingToolkit3DS and 3DS to CIA Converter. 3DS to CIA Converter produces a Rom that will load in Citra but is known to have glitches with some Roms due to its use of ctrtool like causing invisible text for example. I'm told RomFS Extractor/Builder doesn't have those issues which is what lead me to your toolkit.
http://www.maxconsole.com/maxcon_forums/threads/285574-3DS-To-CIA-Converter-v4-1
I noticed that with your first option "Enter D for extract a file/game decrypted" some files get unpacked that are not included again in 3DS Builder, DecryptedManual.bin and DecryptedO3DSUpdate.bin. I don't have the full picture but I also noticed that your method produces a smaller code.bin compared to 3DS to CIA Converter which only unpacks the romfs.bin, exefs.bin and produces a RSF file and exheader.bin (see the .bat under :3dsfix). 3DS to CIA Converter uses ctrtool to do the unpacking, what tool/lines are you using? I can't actually check myself because I don't know how to view the line commands from a .exe.
Personally, I'm just trying to add a patch to a game, but since 3DS to CIA Converter uses ctrtool it has been troublesome. 3DS to CIA Converter uses a tool labeled "_makerom.exe" to actually build the Rom after all the editing. I don't know how it differs from 3DS Builder but its Roms at least run in Citra.
I think if I could just get the untouched exefs.bin and romfs.bin, unpack with RomFS Extractor, edit, pack with RomFS Builder, and then get _makerom.exe to use that, it would work.
I'm looking into using 3dstool instead.
I think I finally got it working with this toolkit:
https://gbatemp.net/threads/the-unofficial-guide-of-nsmb2-hacking.380325/
The key tools are:
RomFS Builder
ExInjector
3DSExplorer