I was able to fix the issue, it actually had nothing to do with the missing items from the scav junkbox. I tried version 1.9 of the profile editor instead of 2.0 and instead got an error message about "mount_aks74u_custom_top_rail_11" from the aMira custom aks74u mod. After removing it from my profile I was able to add items to the stash again both with version 1.9 and version 2.0 of the profile editor.
I have the same issue, my stash is empty except for some thicc cases and like a week ago i was adding stuff no problem, i download some more mods and now i cant add anything cause it says no free slots available, but then i delete the mods i added and it still doesn't work. No idea what's going wrong, and I don't have the mod you had, the Mira custom mod.