hey Gnyxl, sorry to learn of this. I play a sneaky assassin and I basically vacation in that quest when wondering what to do. I am sure you have done all you can so here is what I do anyway:
1) select option two which is the distract one and puts less mobs in the hold
2) I go to starboard or whatever and enter lower area
3) Crest hunt. I click Q and usually spot a few. Locations: In netting (hammocks), by unlockable/breakable door, in room with rednamed pirate. I bluff pull any reapers, sneak down into first room and then open secret door. Loot chest; sometimes there is sentient xp or some rare filigree.
I usually assassinate the active mobs in the hold. If you do things right, the inactive mobs remain inactive and no reinforcements come in. Also don’t fight the rednamed.
Slip into hold, grab any crests there (sometimes even 2); kill rats for second chest option.
Then I go up to lizardfolk area (the door above the tasty ham table). There is sometimes a crest behind the boxes there, and sometimes two will spawn in the lizard room. Bluff lizards and get documents.
If I still need crests, go onto deck. Mobs are 95% of the time facing away, so drop into sneak and go to wizard cabin. Two crests can spawn there. You can loot three collectables too. Don’t fight wizard; no need.
If you are still missing a crest there might be one in the captain’s quarters (sneak easily over to it after the wizard). Gank captain, return to lizard area. Right before leaving lizardfolk to go down below, hit that explosive barrel (this makes them go angry on you. Don’t bother fighting, just leave.) You can then carefully take out the remaining explosive barrels without activating inactive sailors. Check kill count if doing reaper, and if 10, loot.
With knowledge of stealth, you have a chest farm option too—you can hit the two lootgen chests (secret door, cargo area) and loot the end chest without completing the quest. It can be done fairly quickly depending on crest drops. When I am just hitting the end chest, I will avoid the cargo area and check it last as I can sneak to all other locations undetected. It is a lot of fun. You will get rarely sentient xp, some named items and rare filigree like the Dreadbringer ones.
edit: if doing heroic, skip opt chests and just hunt crests. The chest drops the clearwater diamond which is handy for slow heroic healing (16hp/minute) and acts as the diehard feat.
