I really think I went through a lot of similar feelings as you m1469. In other words, I too received Ted's wise advice about cultivating the spontaneous impulse and not worrying too much about theory. But, I too have a particularly strong taste for common practice era harmony. One thing I recall "struggling" with and thinking that I must think about it on an intensely conscious level is modulation. Theory books made it seem so damn complicated and hard to understand. They always interpret the chords before the pivot and after the pivot in two different keys. Personally, I think that's a very stupid way to analyze it. Yes, I'm saying the way we've studied modulation for the past I don't know 100 years? Is stupid. The reason it is stupid is, are we honestly going to think about interpreting roman numeral chords in two different keys at once when modulating during improvisation? Of course not. All one really thinks about during improvisation is introducing a chromatic note/chord. In other words, a sudden change. But, traditional modulation "smooths over" sudden changes by being a change to a closely related key and then re-establishing the key with a cadence as though to say: "yes, we're really in the new key." I found a quote on wikipedia of Schenker saying "there's no such thing as modulation in music." In other words, a modulation is really only a prolonged tonicization. Once I realized this, I understood that I had been doing it in my improvisation for a long time and it is a very simple process. I no longer believe that there is any value in thinking about it consciously, now that I realize how simple it really is. In other words---all the "theory" I've absorbed thus far have had far less to do with creating interesting music than cultivating the spontaneous impulse as Ted has wisely advised. no amount of conscious analysis or willpower can bring about good music just by merely thinking about it. Maybe it can if you write something down on paper and toy with it for months and think about it in excruciating, brow furrowing detail, but, personally I find the idea of working that way horrifying. Partially because I can only devote about a half hour a day to music, I'm more or less forced (though it doesn't feel forced) to cultivate spontaneous improvisation or not create music at all.
Just to clarify/qualify---I think it's fine to go through this stage of wondering whether you ought to be thinking with great struggle about theory---after all, that's what all the universities and textbooks seem to tell us to do (and so one is inclined to give these books the benefit of the doubt...weren't they written by "experts....?"). But if you have as much creative power as I think you do from listening to your improvisations---at the other end of this tunnel will be the realization that all that stuff is smoke & mirrors, hiding the real truth of what creating music is all about. (that's my personal feeling anyway). That doesn't mean "don't study theory," so much as...find a way to study it without absorbing the schoolmaster along with what he has to teach. You don't want an ugly old music theory professor in your brain telling you you're wrong while you're improvising, in other words.
*edit* one more thing. Consider how prolific a composer like Bach was. Has anyone honestly tried to claim that Bach works the same way modern music theory students do when they try to compose fugues? If Bach worked that way I'd bet his output would be an extremely tiny fraction of what he created. The standard modern answer? Bach was an immortal genius, we are mere mortals and cannot possibly imagine the extent of his genius. It may be true he was a genius, but that doesn't mean that we "mere mortals" today cannot find efficient ways of exploring music that do not involve excessive brow furrowing, symbol making and book poring.