Here's what I do:
Typically, I get all 8 quests before heading to the Floating Emporium, filling all those I can from my hold, replacing them until I get all 8 quests where I can only partially fill them with my remaining stored fish. I then sit off the Floating Emporium, and do all my fishing at the market(parts of the docks areas are shallow water some of the time, but not all of the time... bug?).
Once I get all 8 quests filled, then do the following...
1. Deliver any Moonglow and Floating Emporium/Fish Market quests before setting sail.
2. Leave from the Fish Market SW, turning west at the approximate latitude of the Serpent Pillar (this will typically have you sailing over the ocean areas that were once the lower landmass of Haven).
3. (optional) If something has to go to Papua (or if I've already turned in the quest from there), stop at the serpent pillar, cross over, RECALL to Papua (don't move the boat), do your business there, then recall. Check your map to see where you are in relation to the pillar, go to the pillar, and return to the surface seas.
4. Continue W from your return spot (which will be a random direction from the pillar, usually several screens away) until you cross the server line into the waters between Trinsic and Buc's Den. Continue sailing until your map shows that you are past a line drawn down from Buc's Den's west coast, to make step 6 easier.
5. Recall to Skara, Jhelom & Trinsic for deliveries and pick-ups. Odds are you will have to go revisit one of the cities to pick up a quest, after delivering to the other two. Check your quests and their requirements, as you might be able to immediately refill and deliver a quest, before you move.
5.a. If NOW you have Papua's quest open (or get a quest to Papua that you can immediately fill), consider jumping back to step 3 (sailing east from Trinsic waters). Otherwise, proceed to 6.
6. Since (as I advised in #4 above) you are west of Buc's Den (latitude doesn't matter, only longitude), but not so far west that you'll hit islands or swamp, sail due North, until you cross into Britain's waters (the server line passes through the northern part of Buc's Den, through the southern tips of Horseshoe Island). Come to a complete stop as soon as you are clear of the server line.
7. Recall to make your Britain delivery, and to get a Britain quest (by this time, it's almost certain you've turned in your old one from there, as the only old quests left by this point will be to, and possibly from, Vesper). Check the new quest. If you can fill it immediately, and it goes to Skara, Jhelom or Trinsic, sail one screen south and deliver, before returning north, getting another quest from Britain, then continuing.
8. Sail NE from British waters, to reach those of Vesper. Take care not to go so far East that you run into Nujelm or Dagger Island (or sail back into the waters of Moonglow & the Market). Recall to vesper, get your new quest from Vesper, and make any remaining deliveries.
9. Return to your ship, sail SE, taking care to avoid Nujelm and Magincia (especially the latter, with its event spawn). Make course corrections once you pass between those two islands, to reach the Floating Emporium. Dock, recall to Moonglow to get your new Moonglow quest (and deliver any you completed for there along the way), then recall back to the boat, to do the same for the Emporium's Fishmonger.
10. Fish to complete all the quest crates (after all, some areas are shallow water there, some of the time - the area is bugged to where some of the dock areas seem to randomly change from shallow to deep, and back), and start back at step 1.
Note that if you get a bugged quest, just ignore it, and eventually when you go back around the next round or two of the cities, it will clear itself up. It's not worth the hassle of abandoning it.
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