It is normal to have some files in those locations that are not related to Search Marquis. It appears you may have deleted files that were not related to the Malware and the affects on your system are unknown without knowing the names of those files.
If possible, I would recommend restoring to a backup before you deleted those files and post the same locations to get advice on only the specific files that should be deleted.
By following my previous post, the Search Marquis should be gone, but not sure what other files were previously deleted and how that will affect your system going forward. Check the article by John Galt and specifically the last couple of paragraphs to reset the search engine and verify Extensions and Profiles.
Removing "Search Marquis" / "Search Baron… - Apple Community