The cranial rhythm is quite a controversial subject, due to the fact that most people believe there is absolutely no movement along the cranial sutures. While this is true in respects to the bones sliding along one another, the anatomy of the sutures do allow some movement. It is slight and does take practice. In my opinion, the best way to practice is on other heads. It has been my experience (while admittedly limited) that each section of the body has a distinctly unique feel to it. I agree wholeheartedly that improving your ability feel the 'release' in many different indirect techniques will assist with your ability to discern the subtle motions of the cranial bones, feeling the bones themselves move is by far the best way to 'fine tune' this skill.
Anyways, enough rambling...
To answer your questions about feeling the rhythm, I first felt it a couple of weeks ago. It was great to realize that was what I was feeling, as opposed to some of the other motions mentioned. The key to discerning it is making sure you are on the right bones (the vault hold works best for me) focus on feeling them move. If you don't understand the principles involved in their movement, it is more difficult to discern the movement.
In my opinion, the key to successful manipulation is a sound understanding of the involved anatomy, osteopathic principles and a developed sense of what it all feels like.
I hope the above is coherent, it is late and I have spent all day studying Physiology (aka the bane of my existence).
Hope this helps ya.
Ben