Reset Safari as if never run
Solution 1:
Did you also go through the subfolders within ~/Library? Safari files are in a number of different places within that folder?
A view examples:
Caches contains com.apple.Safari and com.apple.Safari.SafeBrowsing
Containers has multiple com.apple.Safari folders (may not exist on 10.11.6, I don't have anything with that OS to compare to)
Preferences, etc.