If following the Dark Brotherhood attack, speaking to a guard on the mainland, they will redirect the player to Senillos Tulnus in Firewatch, who in turn will redirect the player to Garros Mellorus. However, these still trigger the Vanilla journal entries, asking the player to go to Appelles Matius and Asciene Rane, which is both misleading and confusing. I suggest adding new entries to the journal for the Tamriel Rebuilt-specific path of this quest.
I noticed you made some tweaks to this script following this bug report: https://www.tamriel-rebuilt.org/bugtracker/coldharbour-keelhaul-will-not.... However, if following Noga-Togroi's instructions and keeping the spear (he says Molag Bal lets you do that after all), the player still gets teleported to Baelkashpitu after three days, and you get a journal entry that you have failed. This happens despite the quest being marked as finished, so something is obviously wrong with the script.
This is by far the worst implemented quest I have played in Tamriel Rebuilt so far. Given that it is one of only two side quests starting out from Firewatch, it could certainly use some improvement. At least the following issues should be addressed:
When completing the quest "The Exiled Duke's Affair", the player is rewarded with a really powerful amulet. Given that this quest can easily be finished already at low level (unless there are any level modifiers, I haven't checked) and you will keep this for the rest of the game, I think this reward is a bit too powerful (it can easily be compared with some of the famed artifacts). For a more balanced experience, I suggest reducing the effect to Fortify Personality 10 pts, which is already very good for a constant effect item, and would certainly be useful for most players.
The sttarting script for the quest "Muskflies in Bal Oyra" does not begin until the player arrives in one of the Bal Oyra cells, causing quite a problematic behaviour if first arriving in Bal Oyra from the road. The script makes all the NPCs disappear, but this doesn't happen until you have taken a couple of steps into the town. I was even talking to one of the NPCs at first and then they all just disappeared, so this is both confusing and unrealistic. This should be solved somehow, perhaps by starting the script already when the NPC arrives in one of the adjacent cells.
The door in Firewatch Palace, Duchess' Quarters, on the lower floor, which is supposed to lead to the lower balcony, spawns the player at the wall underneath the palace tower, several metres below the intended location.
When asking about "specific place" in Tel Branora, the NPCs will tell you that the ship offers travel to Ebonheart, Vivec, Molag Mar, and Sadrith Mora. With the new travel network introduced by TR_travels, this should be updated.
Extremely minor issue. A single line "spoken" by Pelagius the Rat in Old Ebonheart, Ruma Soanix's Manor is missing two commas.
[Despite its whimsical name Pelagius the Rat doesn't seem to be one of those extraordinary rats that can talk. Or maybe it can and it's just choosing to ignore you.]
Should be:
[Despite its whimsical name, Pelagius the Rat doesn't seem to be one of those extraordinary rats that can talk. Or maybe it can, and it's just choosing to ignore you.]