I think you should put all this in writing, all the issues, the phone calls, with as much detail as possible, also telling them about the over payments, in a letter & send it to them. In that, ask them where do they want to go with this now, tell them you expect a written reply within 14 working days - failing to do so will result the surplus monies been "given to charity". The "charity" in question can be anything you want it to be...even you own back pocket.
This moust have caused a huge amount of frustration for you... I don't think I would be as calm as yourself if it took that long, with that hassle to get your money back.
Good luck with it...