the dealer will not be able to help you with this. the only way they could try and and do it is to force feed it the as built data from a 5-speed car. If somebody from the tech hotline wanted to help they could do it with the hotline engineer telling the dealer what lines in the as built data to change. I had to do this once for a focus that thought it had abs.
the way to go would be contact a local tuner. they can handle this problem way easier. might be pricey but eaiser.