It has been awhile since we have seen you in Richmond! James is doing well. His speech seems pretty normal to us at this point (maybe some subtle things remaining). I was emailing with a related question, and hoping that you can point us in the right direction.
James has had some issues in the past with "mouthing" things (for lack of a better word). This seems to wax and wane, but in the last few months, it seems to be significantly worse. He will either have his hands/fingers/thumb in his mouth, or water bottle, pencil, swim cap and goggles, etc depending on the situation. It seems to be something that he does unconsciously, despite our attempts to call his attention to it, even trying "penalties" for having his hands in his mouth. Lately, I have noticed him doing even while talking to his friends, while playing soccer (when there isn't any action near him), etc. He is 11, so it is an increasingly odd behavior than it might have been at age 2. (We haven't noticed any other odd behaviors or habits, just this one...and otherwise he does well in school, socially and in sports).
We aren't sure what the next right step is to help him be able to stop this habit. Deterrents don't seem to work, other than to stop it while it is happening, and I wonder what the root cause of it actually is. I am not sure that a regular speech therapist would be there right person. Do you have any thoughts on how to help him?
The situation you describe is often seen with individuals who have innate muscle weakness. The habits seem to come and go and can take many forms as you mentioned above. Last time I saw him (May 27, 2012) I recommended a gum chewing program. I use gum chewing as outlined in the book Assessment and Treatment of the Jaw for both improving muscle skills in the muscles of the jaw and as an alternative to the "habits" you describe. There are more nerves going through the Temporo-mandibular joint (TMJ) than any other place in the human body. It is where we go for calming. Babies suck their thumbs, bite on their fingers, rely on a pacifier, etc, to give stimulation to that joint.
James may also need to give stimulation to that joint for calming and that is where gum chewing comes into play. If he does not know how to chew gum without swallowing the gum you will have to teach him this motor plan by going to that activity in the book Oral Placement Therapy for Speech Clarity and Feeding. In it you will be given a step-by-step program which I have used with children as young as 2 years of age.
Once he can chew independently use the gum chewing as an alternative to the "mouthing." I hope this answers your question. Please tell him I said "hello."