Dear David,
Thank you for sharing your experiences. They are not at all unusual, and you are not doing anything wrong.
The noise that you are experiencing at the beginning of your sessions is just the same interference or distraction that our stresses give us all day long (see
http://www.nsrusa.org/about-stress.php for details about how and why stress does this).
You are doing just the right thing at the beginning: not thinking the syllable when it would be difficult to do so. In fact, if you were to think the sound by force, you wouldn't transcend at all. There would then be no opportunity to release the stress that limits your functioning.
In the middle, it sounds to me that you are experiencing clear transcending, both the inward and outward strokes, as described in the NSR manual. Naturally, this is more enjoyable than experiencing only the side effects of stress release, but both experiences are necessary and valuable.
Near the end, all the deep rest that happened in the middle allows the nervous system to resume releasing a very deep stress. Again, the mantra is not important during this period of stress release, so don't worry that it is not there. Be glad about the discomfort, because it shows that your meditation is really working. If the discomfort gets too uncomfortable, add two or three minutes of mild stretching or easy Yoga asanas before each session and add five minutes more rest at the end of each session.
As time goes on, your experiences will undoubtedly continue to change in various ways. Just follow the NSR instructions and good things will follow.
David Spector
NSR Meditation/USA