Tinwoo is stored in /switch along with the rest of the .nro homebrew. Not going to impact Tinwoo in any way.
Yup…Kraft in your old directories can cause this. When a guide says
remove the /atmosphere/contents and /bootloader directories, you can simply rename them to /atmosphere/contents.bk and /bootloader.bk respectively. This ensures you can boot to a known good state. Then you can start moving items back and rebooting to test everything still works. Move things in small batches in case there is a module or something that breaks things. That way you can easily back it out and only have a few things to research for a fix.
In your case I would suspect that your Sigpatches are funky:
Sigpatches — get your iTotalJustice Sigpatches here (with free instructions!)
Sigpatches (GBATemp) — alternative Sigpatches for when others don’t seem to work.
or
Maybeeee your fusee.bin doesn’t match? (really reaching on this one)
Make sure you download the fusee.bin from the same repot and release where you got your atmosphere.