It is illegal for medical providers to enter into a percentage based contract in the state of NY.
As far as references, be honest but at the same time give them some personal or other professional references, nothing wrong with that because the provider may want to check things like dependability, trustworthiness, etc.
As far as her wanting the diagnosis to get "around" the Medicare cap.. that's a no no, she should code as per her documentation on a patient by patient basis. Billing and changing codes for the sake of reimbursement, is a sure fire way to end up in hot water, same for you since it would land you in trouble.
Some things I would do is find out exactly what problems she's having with the present billing company and focus on those areas where you can make a difference in her practice.