Well today we were finally able to get him into a specialist.
The doctor came in and had me set him down on the floor without shoes so he could watch him walk. Immidiately, he noticed a problem. He sent him for xrays and shortly after came in with them. He said he has never seen a case like this in a child and has no idea exactly what it is. He said its NOT club foot and not pigeon toes...well not on his really bad foot. His not so bad foot is a teeny bit pigeon toed but not enough to need any care.
He also said that regardless of WHAT it is...the most likely fix is surgery. He doesn't feel comfortable treating him given the circumstances, so he has referred us to a better doctor. Specifically a PEDIATRIC orthopedic surgeon. The chance of surgery is high, but they will not do it until he is 5 or 6. I will post pics in the comments of his xrays so you all can compare good foot to bad foot.