... do you think about the story/kanji in your head, and when you're happy write it down? Or do you write down primitives as you remember them?

I tend to get annoyed with myself it I have to stop half-way through writing a kanji to think about it again. But then again I don't want to spend 10 minutes trying to think of a kanji.

i never pay attention to how much time I spend per kanji.

I study for as long as it takes to remember it. Sometimes it's very short. Other times it takes a while. Better to get the kanji memorized well instead of re-studying it a million more times.