Miklkit - I hope this helps.... If it is too confusing just ignore it.
Not sure where to start so this may be a little mixed up. Any way here goes:-
The side quest are independant of the main Storyline
Elizabeth Shaw - This is a side-quest - the main locations involved are Cayman, Antigua, St Martin and a short stop in Guadeloupe . If this quest is broken then it should not affect the main quest - hopefully. Since it does not use these locations - I hope
Artios Voisey - this is a side quest ( from the original game ) - If Artois was killed ( sunk ) before he took you to the treasure wreck then the quest will not finish. After he takes you there he becomes an officer / passenger just like the ones you hire, and Quest book header should close. Then you can give him a ship, until he leads you to the treasure it is best to keep him walking arround with you. ( and alive , of course )
:
The saga of the Blaque family is a side quest - involves going between Port Royale, Jamaica & St Pierre, Martinique. ( shuttling between family members )
Fred Bob (Help the Boatswain ) and its sequel Help the lady are also side quests. Help the Lady invloves going to Puerto Rico and Nevis Pirate settlement
Find the Traitor Raoul Rhiems is part of the main storyline & Deliver a closed chest is a small quest within the main storyline.
Since you have found both Fred Bob and the Blacques side quests - you will have met Orable Caron - he is the start of several side quests so be careful what you say to him.
On a purely personal basis ( and everyone plays the game differently ). Assuming Elizabeth Shaw & Artios Voisey are broken, I would ignore them.
I would try and complete the Blaque family and then continue with the main quest.
The problem with your reputation - if you can't get to a Governor and buy forgiveness from them.
You could try to find a diplomat ( usually in Pirate Taverns - Nevis P.S. : Tortuga, etc I think the tortuga one is in the townhall ? :? ) - they can improve your relations for a price.
Lots of money
For your information the quest book headers for the main storyline are ( in Order ):-
Inform the Governor about the French Attack
Reconnoitre captured Speightstown city
Escort Troopship to Barbados and Meet Spy
Deliver a Closed Chest
Wait for new orders from Silehard
Get out of Jail
Find the traitor named Raoul Rheims
Deliver a letter to a pirate chief
Return the native art collection to Governor Silehard
Deliver a Prisoner to the Governor
Rescue Researcher
Continue searching for Rheims
Find Danielle
Get details from the governor
To San Juan
Meet Danielle on San Juan
Repel the English Squadron attacking Bridgetown
Sail to Cozumel with Danielle and Aurentius
Sneak into Temple
After Final
The side quests Headers - in no particular order are:-
(these are independant of the main storyline )
Sink the Pirate Corvette
Saga of the Blacque Family
Help the Boatswain
Help the Lady ( sequel to help the Boatswain )
Saving Toff’s Daughter
Cargo for Thomas O’Reily
Smuggling for Thomas O’Reily ( Sequel )
Patric and the Idols
Artois Voysey - cancels Nigel Blythe
Nigel Blythe - alternative to Artois Voisey
Escort Vigila Mendes Ship
Zaid Murro’s Problems - sequel to Vigila Mendes
Hard Labors of an Assassin - if you trigger this one do it before continuing the main story as this one has time limits and consequences if it is not completed. ( see Walkthrough in Wiki ) - bad people chase you and try to kill you
The French Pirate in the Tavern
Rescue Bartolomeu o Portugues’ crew
Search for Bartolomeu’s ship
The Silver Train
Help the Turks Island Settlement
Find Angelique Moulin’s Father
A girl won in a card game
Elizabeth Shaw’s Disappearance
Find the missing son of the Spanish Admiral
Strange things going on in the Caribbean
Help the Church - part of Strange things going on in the Caribbean
I hope this helps - if you get really stuck take a look at the walkthrough on the Wiki.