sorry to disagree; I see nothing "below board" or unethical about what your doc is saying. He is practicing "full spine" adjusting. There are many doc's who feel that adjusting the entire spine is beneficial. some doc's limit themselves to the primary chief complaint only, orthers address the entire patient-to include any associated area's. If his daily treatment notes/ records can back up and justify his approach--don't call him unethical.

he was incorrect in continuing to bill E&M along with the CMT codes, you correctly pointed that out, and he agreed.

I feel this is more a case of you and your doctor client not understanding each other, as opposed to a legal or ethical situation. My advise would be to sit down together and attempt to meet eye to eye. explain to your doc that in order for him to code as he does he will need to justify his procedures via his case history and examination. I'm sure he'll see the necessity of this. then allow him to better explain to you why he does what he does. I am certain the two of you can come to a meeting of the minds.