If you need that girl to stop it than I can't. I didn't have Jan kill her (maybe I should've) but I don't have her anymore. She up and disappeared from my cabin from being at sea for to long so if I needed to talk to her than that is how I'm bugged on the rep.
Damm matey...
You massed up with the game already! Remember this game is hardcore and there are many 'restrictions & condition' to complete any mission.
Like for example: there are 3 ways to do Dutch Gumbit. But if you cross concert level then other 2 ways will be close for you.
Path 1: "The passage of the Dutch gambit for the Secret Organization:
*Character level not higher than 15.
*all 3 swords + firearm skills at 25 or above.
*Finally, you need the
second negative reputation level."
Path 2: "The passage of the Dutch gambit for England:
*The game for England is designed to pass the hero of 13-14 rank.
*Requirements for the quest: SG not higher than 15 rank, navigation 30, honor - neutral or positive."
Path 3: "The game for the Dutch West India Trading Company (GVIC) is designed to pass the hero 10-12 rank. No requirements for taking the quest."
**Only path 3 is always open. So if you cross level 15 then other 2 path will be closed for ever. Another thing Dutch Gumbit only trigger after 3 month from last meet to Michel de Montpe.
Here I said about restriction and condition only for one mission. There are for every mission. So be careful. Don't mass up.
As for FTJR or Under the Black Flag there are condition too.
Merabel is very important character for FTJR. You must not kill her before. And she will die if she stay at sea for several days(that's why you loose her). Immediately bring her to Isla Monet (your privet island). She lived there for ever with other 3 men. Those are very loyal to you. You can visit her time to time and do sex (have to say) with her.
And only she can stop that negative reputation problem after FTJR. Its completely story made. After you have Merry/Helen on your ship permanently, she will stop doing 'good' things with you. But lived there for ever.
EDIT: Hero have to talk to his brother too, after Merabel.
Note: In that home you can store all your loot too. There are some big chest (including underwater secret one). Merabel will take care of them.