Douglas, You might be interested in what the AAP has to say about the role of pediatricians in helping children and families deal with separation and divorce. I've pasted an excerpt below, which seems to describe your situation. I think it is natural for third parties to feel like they have to take sides in a situation such as this, but aligning with one side or another---unless there is clear evidence of negligence or abuse---is not necessarily in the best interest of the child. I think Julie H. has some very wise and poignant counsel to offer you and I hope that you and your ex-wife are able to find some mutual ground on behalf of your son.
"....In contentious situations, the parents' anger may result in the child being used by one parent against the other, serving as a messenger because the parents are incapable of communicating directly, or suffering for lack of financial support. The pediatrician should be careful not to take sides in a divorce dispute unless there is clear, persuasive, firsthand evidence that one parent is unfit to care for the child. However, the more common circumstance is that the parent with the best relationship to the pediatrician will ask that a letter be written to the court that supports through secondhand information or hearsay the contentions of this parent against the other. In most circumstances, the pediatrician should refuse such requests, maintain an appropriate relationship with both parents, and advocate for the child to be protected from parental hostility....."