Hi NickR,
I am so glad for you that you have got off to a great start with Brain Ev.
Perception is an interesting thing. You wrote that being more aware of your thoughts is a "side effect". In my opinion, side effects are undesirable effects of, say, taking medication. Surely being more aware of your thoughts is a BENEFIT? People meditate for years and years in order to become more aware! That is considered in many circles to be a highly desirable trait.
Regarding your neck pain. I cannot answer from personal experience, so these are mere suggestions. You have three options.
Do your Brain Ev despite the pain and observe what happens. You may find you still entrain well. Or not. Worst case is you manage to relax a bit.
Or you wait until you are better and continue where you left off. Again this is personal. It is a choice. As you have adapted so well to level 1, you may just be able to continue seamlessly.
Or you may prefer to 'regress' a little, treating the whole Brain Ev program as a mental workout. Just as with a physical injury, you would restart training a little gently and tentatively. For you this could be restarting Level 2.
When the time comes. listen into your innerself and see what prompt you get. Follow your intuition. Try that and observe. After a day or two, you can determine what is the most beneficial course of action for you.
Hope your neck feels better really soon. Happy journeying, Pure Bliss