Kendrik, sorry I missed your post the first time. Here's my response.
Short answer: Yes.
Will these things (proper techniques and form) become more instinctive with practice and experience?
Long answer: Yes, but you have to understand that as you drill in the basic movements, you'll improve your all-around game. Work the basic techniques and understand the basic concepts before you start to jump too much into the theory of the style, otherwise you'll make your problem worse.
Is it likely (again, including practice as a factor) that the disconnect betwen mind and body will be reduced in time?
Also, what things would you recommend I do to work on flexibility? I'm rather bendable considering my relative lack of fitness (helpful in being able to resist an early tapping), but I have a hard time manipulating my body (my legs in particular) to gain a better position. Any tips?
Practice using the rubber guard without an opponent. That is to say, pull your instep to your forehead in order to mimic kung-fu-move. Also practice the basic stretching regularly, along with your conditioning. This will improve your game alot.