INSTRUCTIONS:
The relevant folders should be located at the equivalent to C:\Program Files (x86)\Steam\steamapps\common\Sid Meier's Pirates!
- back up your Pirates!.exe and replace it with the provided version.
- Place text.ini into the "assets" folder within that Sid Meier's Pirates! folder.
- Place the rest of the files into the "custom" folder
They can be within a further subfolder if you wish to organize your mods that way. I believe that the game loads any conflicting files from different subfolders alphabetically, with the last taking priority.
Regarding a false virus alert:
It does include a custom pirate!.exe
(hex edited which AV hueristic pattern scans may not like)
If using Firefox Browser
check Tools - downloads
confirm if the download is blocked and
right click on filename to unblock
or alternatively your Anti-virus console log (notifications)
or Quarantine Area
(sometimes called Virus chest)
and restore to unblock file