[HareBrain]

That's a big, big improvement Waffles: exactly what I was hoping for . Now we can get down to the real nit-picking. *rubs hands in glee*

Before that, just one thing. The line "Zachary stared back and finally spoke" near the end - there's quite a lot going on in his mind at this point, the decision he has to make, but we don't get any idea of that until the next paragraph. I think some hint that he is making a difficult decision might be useful here.

Now for the nit-picking. I still find myself disrupted sometimes by your punctuation. I personally would put more commas.
Eg:

A funnel shaped like a squashed hourglass connected the murky depths below to the ragged, swirling span of clouds high overhead and he was certain to be the only fool to ever venture this close to the awe-inspiring and terrible spectacle.

I think there needs to be at least a comma before "and he was certain". Personally, I would make it a full-stop (I would also join the description with the previous sentence). In fact this is what I would do:

Such an ancient, terrible thing that it was, like a hundred thousand hurricanes angrily swirling within the aether; a funnel shaped like a squashed hourglass connected the murky depths below to the ragged, swirling span of clouds high overhead. He was certain to be the only fool to ever venture this close to the awe-inspiring and terrible spectacle - that he had done so at the request of another fool with money made him feel all the more foolish.

Or something like that. Another example:

He turned to his steward, “Go check the barometer if you would Mr. Gesse. I need to know where it is at and whether it is rising or dropping ” he asked.

He turned to his steward. “Go check the barometer if you would, Mr. Gesse. I need to know where it is at, and whether it is rising or dropping.”

The comma after steward would be OK if you'd put: He said to his steward, "Go check ...", but "He turned to the steward" is a sentence in itself. I've added a couple of commas, see if you think they make it flow better. (You also don't need "he asked" tacked on the end like that.)

He then addressed another man coiling rope on the foredeck, “Mr. Christian, would you be so kind as to fetch Mr. Lawrence from the boilers? I need to discuss our fuel situation with him.”

Again, the comma after "foredeck" should be a full-stop, or actually you could use a colon here (well, I might. Some would disagree.)

The man waved at him to confirm the order and jogged for the nearest hatchway. Looking back to the Maelstrom, and the smaller storms it was spawning, he wondered whether or not his ship could survive contact with such things. He knew damn well they’d never be able to circumnavigate them on the timetable his patron had given him.

I've added two commas here and changed one to a full-stop. I guess the theme here is that I think your pauses need upgrading! Otherwise it reads in a bit of rush. Hope this makes sense? Please ask for any clarification!