One of the things about NEW is that the sensations are usually stronger than most other types of energy work. (Yes, I know it's an individual thing, so people please don't pm telling me it's not so for them ) If the energy sensations are so strong they are uncomfortable I'd say take a break from doing them and start at another time. However, I know this may not be what you want to hear, since you have the CD and want to use it to follow the program as it's designed.
I would recommend a few things: If the sensation is one of pain, then definitely see a doctor to see if there are any underlying physical causes like autoimmune desease, arthritis or something else (stranger things have happened). If what you are experiencing are twitchiness-type things, then the culprit may be the combination of the binaural beats with the energy work- too much for a very sensitive person. If this is the case, I'd recommend that you do the energy work separately from listening to the CDs (yes I know it's hard, but you can try it that way) and see if the sensations diminish or are not so disturbing.
Achiness sort of sounds to me that it could be energy drainage problems (your energy body is out of shape)- but not pain though. So, if it seems to be exhaustion, take a few days off, get a lot of sleep and try it without the binaural beats.