Your process is VERY different from mine, so it's difficult for me to figure out what's really causing you trouble. (For example, I don't worry at all about message when coming up with a story. I don't even worry about storyform really, other than trying to get a sense of what the different throughlines are. My criteria is basically just "coolness" -- "does this seem cool? do I like it?" This doesn't change once I'm working from a storyform either; what the storyform does is to align my thinking. Oh, and sometimes it helps validate ideas -- seeing how stuff matches up to the storyform gives me more confidence. But anyway, that's just my process -- lots of people do things differently.)
Still, even taking into account the differences in the way we approach story creation, I sense something is off when you say:
I think it's totally okay to look at an idea your subconscious gave you and say, "nah, not quite right" or "try again" or even "WTF??!" However, to say "ooh, I really LIKE this idea ... but it's not right because his fears SHOULD be proven false" ... I don't know, there's something off about that for me. If you really like something and want to write it you should go for it! Screw what the fearful, analytical part of you believes SHOULD happen -- maybe it's wrong.
That's what I was trying to get at when I was asking what you love about the story. I think the things you love about it belong in it; they're the core of your idea. They take precedence over any storyform or "message" because you're never really sure what those are until you've written the thing.
Here's what I think you should try. Make a point-form list of all the different things you love about this story. Stuff you're sure about, stuff that you only toyed with, but only stuff you love (or at least, really like and would want to write about).
Because you seem to have a good handle on your MC and IC, the first three items of your list should be 1-2 sentence summaries of your MC, your IC, and their relationship. Don't worry too much if some of their issues might be more in the OS; just do your best.
Then the rest of the list will be all the other cool ideas you have for the story. It's okay if some of them are contradictory. Story ideas only here, nothing about Dramatica, structure, or message (at least not directly; it's ok if you can see an aspect of theme or something behind the idea).
Finally, when you're finished the list, ask yourself how those items could fit in the overall story that the MC and IC will get wrapped up in? Let yourself daydream, pick and choose, and do NOT worry about structure or message. If blue-collar necromancers sounds cool, explore that a bit. Make some notes on how that might work.
Hopefully this will get you thinking on what the whole story could be. Let it gestate for a while, solidify, and only then start looking at how it fits into a storyform. Possibly. You might be better off just starting to write with the vague ideas of the throughlines in your head, kind of egging you on and inspiring you because you're wondering what they really are...
P.S. Love the idea of the zany tone. I'm picturing something a bit like A Series of Unfortunate Events which is brilliant. Go for it!