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Pirate quest is for when player manually hire the pirates to attack another player. This does not typically happen that often.
Warning time is the countdown bar from when a raid launches to the bidding period of the next raid. Min/MaxSendRaid is the range that the pirates will wait to accept bounty, after the warning has been given.
And if I change these files in a mods folder does that change just the mod or do I need to change these files in Sins main folder?
NEVER change files in the Sins main folder.
If a mod does not contain a copy of the file you need to edit (gameplay.constants in this case), copy it from the Sins main folder and make a new folder in your mod directory. Copy the file structure and paste the file in your new mod folder. Then edit that copy (I.e., make your change in a mod). This prevents you from screwing up your game with a bad change, and lets you toggle your change on and off if you like.
If a mod does contain the file, you can either make the change in that mod's file or do the same steps as above, but with the mod's file. If you play MP with other people I recommend the full make it a new mod, so you can toggle it off to play with people online.