I could drum something up. Have Malakaus get out of the water and confront Noelle, cause a scene. Or maybe see that she left, calls off the operation, heads towards the forge to start working on making copies of his crossbow.
Say Commander, how long did you plan to have the ship waiting in Khenarthi's Roost? I'd say it should take at least three days for the entire crew to finish up working on the ship, like the repairs, renovations, armoring, etc. During the mean time I also planned to have Malakaus talk to either Sharee or Noelle about their knowledge with explosive alchemy so he could try to create balista bolts with something similar to them. Or even invent the cannon himself if he can figure it out.
I'm also thinking about upgrading the crew's equipment to something a bit more standardized; Chainmail made of elven metal for those who want to use light armor, Elven plate for those who want to use heavy. Also if he can get his hands on a lot of soul gems (Doesn't even need to be powerful ones) he could start making jewelry for waterwalking/breathing for everyone. Given that we would be operating mostly on a boat, I figure this would be important. Just be careful of you fall off the ship; I think you take fall damage if you land on the water while having waterwalking active. I'm also thinking of getting Fletcher to catch wind about a Dwemer Ruin; this is so Malakaus could get his hands on the dwemer metal and turn those into weapons. Of course, he'll need help bringing out all the scraps, and I don't know if the Dwemer ever had places in Elsweyr. Also I'll be having Malakaus create copies of his box-fed crossbow. By Skyrim's count, I'd say he'd would be making weapons around level 12 or so, Elven armor and Dwarven Weapons. I'll also have him or his Argonian's start inscribing some spell scrolls, that way even the magically inept can be flinging Ice Spikes and such.
I'll also have Malakaus start training some of the crew with his skills. Which means more heavy-armor and shield-fighters. I definitely know that his Typhoon Warriors are going to be this anyways. He'll also be taking anyone with the interest to learn how to scribe scrolls and enchant as well. No sense in letting him get bogged down in menial work.