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Ford has released a service bulletin that deals with diagnosing the sliding door system that may help you diagnose the problem you are having. I have enclosed it in the link below. It would also be useful if you can scan the BCM (bldy control ) module and see if there are any B fault code setting which would narrow this down. Post back if you can get me a fault code and I will have a look for you.https://dl.dropboxusercontent.com/u/104923897/Sliding%20door%20Sept%2010.pdf
The steps to check it should be included in the steps in the service bulletin.