Which installer did you use? It looks like you've mixed two different versions of the mod.
The current one, dated 31st August 2017, can be found by following the links in post #1 of this thread; it is held on the Pirates Ahoy FTP site. You'll also need the Beta 4.0 Part 2.0 Contents Archive file, also linked from post #1 of this thread; that file will come from ModDB. Download both these files, and optionally also my updates archive, also linked from post #1 and held on the FTP site. Re-install the stock game from CD, then run the 31st August installer to add the mod. Then you can unzip the updates archive and copy everything from there into place.
The current one, dated 31st August 2017, can be found by following the links in post #1 of this thread; it is held on the Pirates Ahoy FTP site. You'll also need the Beta 4.0 Part 2.0 Contents Archive file, also linked from post #1 of this thread; that file will come from ModDB. Download both these files, and optionally also my updates archive, also linked from post #1 and held on the FTP site. Re-install the stock game from CD, then run the 31st August installer to add the mod. Then you can unzip the updates archive and copy everything from there into place.