There is no "Tortuga citizen_dialog.c" in your zip file. Besides, if there's one file in which "Tortuga" should be hard-coded, it's a dialog file specific to citizens of Tortuga! So then I wondered if perhaps the file in question is a more generic dialog file. And that led me to "Enc_Walker.c", which does indeed have the change from checking Tortuga to checking "relation_to_pirates". Testing is very easy. Change 'switch(chance)' to 'switch(1)', which will force any random walker to check you for piracy. Start a FreePlay as a pirate. Before sailing away, go on deck so you can hoist a false British flag because random ships near Nevis are likely to be British or allied and you don't want to waste time fighting or running from them. Then sail to either Port Royale or Port au Prince - remember to hoist an appropriate false flag! Talk to any civilian carrying a weapon. If it's "Spanish Main" period, both towns are friendly to pirates and you should get the "Greetings, wayfarer. Where are you going?" dialog. In any other period, both towns are hostile to pirates and you'll be denounced. Except that you'll find the dialog crashes out with a blank box because you used 'CheckAttribute(rPeriod, "Towns." + GetCurrentTownID() + ".relation_to_pirates")' and you didn't define "rPeriod". I replace "rPeriod" with "Periods[GetCurrentPeriod()]" and then it worked perfectly, both in "Spanish Main" and "Golden Age of Piracy".
Perhaps I still had some of the files from your previous update. So I simply wiped my "Pieter_fix" folder, downloaded the zip again and unzipped it. There are still some obsolete files, though. For one thing, a lot of dialog files still have the wrong boundary between night and day.
More seriously, there are some questbooks in "RESOURCE\INI\TEXTS\SPANISH\Storyline\Ardent" which I don't have. That's because they're supposed to be in the "QUESTBOOK" subfolder, which is where I do have them. Also, you have "RESOURCE\MODELS\Locations\Inside\Dungeon1\d01_l_Bathhouse.gm". It should be in "Dungeon_1", not "Dungeon1".