Reset Safari as if never run
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.