My son's ex took out a loan for his car (registered in his name).She asked him to sign the car over to her for sale.Who pays excess owed?

If the loan was taken out in the ex's name, then she's the one liable for repayments. It looks like the car actually belongs to the ex from what you said because your son is only the registered keeper and not the actual owner. He does not have rights of sale on the car and if he takes over the payments for the car and settles the finance, he won't become the legal owner.

You son doesn't have any proof that he purchased the car right? It's the ex who has it, in terms of the finance for the car being in her name, right?