Thanks for the honest response, Sean.
What I meant was that if you understand what the Main Character Throughline is (a first-person perspective or worldview on personal issues)... and you can see and write down how the source of the Main Character's issues is Activity (Physics), Obtaining, and Self Interest ... then when it comes time for you to illustrate the Main Character's Problem of Pursuit, you'll be fine -- you won't have to worry about the 'flavor' of Pursuit.
If you get the 'flavor' of Pursuit wrong, it won't be because you got Pursuit wrong, but because you got Activity wrong. That's the reason it helps to go from top to bottom -- as you zoom in on the various levels of conflict, you align yourself to what's really driving things.
Does that make sense?
Regarding uncertainty about how to use elements, etc., remember that there are a LOT of "right" ways to use all the different elements -- there's a lot of overlap. If you think you're exploring a particular element, and you like that part of the story -- then great, you almost certainly are exploring that element. Even if you were wrong, the whole point is to tell a good story so if it still works, just go with it.
Also, on this:
If the storyform isn't helping, put it aside and just write (or plan your story if you aren't ready to write just yet). It may be that the storyform isn't the right one, and the only way to get to the right one is to tease more story out of your right brain (aka Muse).
When I say put it aside though, you don't have to put everything aside. If you're certain your IC is in Situation, for example, then you can definitely keep that in the back of your head. That way when you suddenly realize the IC was part of a human cloning experiment you can nod your head and say, "good idea, that fits".