I'm stuck....completely

[YaoriChan]

I think I'm pretty far in the game; I've finished many quests and only have a few left. The problem is, I can't do anything to complete the last remaining ones. Those left include:
- A change of plan
- The king of Muridea
- Vessels of the gilded warrior
- The five smugglers
- Unmasking the master
- The lost squad
- Beetle hunt

Now, I don't care much for the king suit, I can do that later on, but I can't finish any of the quests listed here:
- A change of plan: every time I go see the commander, the conversation won't go further than him telling me that I sung my song wrong. Every time I sing something else, the answer remains the same.
- Vessels of the gilded warrior: I have to do something first so that I can access the last urn (which I don't know what that is).
- The five smugglers: I have to fetch the key of the last smuggler, which is the one in the kitchen, which the cook owns and won't give to me. I heard that I have to get the help of Sileas in order to unlock some new conversation options, but Sileas won't come out of his room since he helped me with the message to Merra. Also, I didn't complete the beetle hunt quest, which would've given me the key to his cot. So now, I can't complete those two quests.
- Unmasking the master: I don't know what I'm supposed to do for this. I talked with every guard, even the smugglers, and none of them have given me said evidence to prove that the cook is the master. Again, if I want to have new dialogue with her, I have to talk to Sileas and I can't do that.
- The lost squad: I've searched, literally, everywhere in the catacombs, and only ever found one of the squad members. I don't know what to do at this point.
- Beetle hunt: Sileas is in his cot, so I can't talk to him to finish the quest.

Can I be guided through this a little bit please?

[Omegatherion]

You can only advance in the main quest right now. All the other quests will be doable once you reach a certain point there.
You need to get a book from the harbour (it is in a shelf right next to the big table) and then talk to the two mice on the ship again. After that you can go to the commander and let him sign the new route for the ship.
Once this is done, there should be a guard at the spot where Silas usually is. He will tell you that Silas is in the kitchen. From there on you should be able to continue.

[YaoriChan]

OMMGGGGG THANK YOU KIND SOUL