Unless I'm distracted by something else (sometimes even then) the thoughts are always there. Even in the deepest periods of denial in my life, I still always thought about it. At times it's a form of background noise in my head, just subtle feelings that shape my more conscious thoughts. Many times however it's actual conscious thoughts about how much I wish I had a female body, how much I hate feeling the need to be something else, feelings of wishing I could just rip my skin off, fantasies of having a magical power that gave me the ability to turn into a woman, etc. I can become very distracting at times.
As I've more recently stripped away the denial and conditioning, it has gotten much worse. Now that I'm more connected with my feelings and allow myself to acknowledge them, I think about it deliberately even more often. I also have more triggers. Just seeing a woman in a cute outfit that I'd like to wear, seeing an advertisement for makeup or shoes or Fabletics or whatever. Sometimes just being in a room dominated by men (like at work) can even set my thoughts in motion.