When you say "an old stone house in the old part of Rethymnon" I'm assuming you mean the old city itself, not in the wider nomos? And I'm wondering how extensively you've researched the idea, because it wouldn't be everyone's idea of location for a home. To be honest, it wouldn't be mine, and I know the place pretty well.
When the American anthropologist Michael Herzfeld was researching his book about the old town (A Place in History, published by Princeton University Press in 1991) he found that many of the residents longed to move out to the modern, airy developments of the new town like Kalithea because their lifestyle was inhibited by suffocating planning restrictions.
That book was published a quarter of a century ago and I don't know what is the current situation re planning, but it does look as if the conservationists are winning a long-running battle: the historic infrastructure is remarkably intact and one suspects that it may be at the expense of people living in those narrow streets.
You can't move for tourists in those streets in summer, when it can get swelteringly hot in the old town. The drainage system is ancient and inadequate, and the town is seriously smelly. When I first knew the city, there were several "proper" shops to service the locals. One by one they have given way to boutiques and cafes.
Also in the summer, those streets are mostly closed to traffic. So you need to consider how easily you are going to be able to remove rubble from your old stone house, or to import building materials. Will there be restrictions on the noise your workers can make? How possible will it be to park your car near your house? How far will you have to carry the weekly shop, given that there is only one small supermarket in the the old town itself? When it comes to restoring/building your house, are you going to be prevented by planning restrictions from adding some of the features you'd like?
There's a lot to consider and you certainly need expert advice. The company recommended by Mouche is well established in the old town itself, and I'd also recommend http://domisidevelopment.gr/en/
It may be that you particularly like the idea of a house in an urban environment, but I'd urge you to look further afield, to some of the old villages in the Rethymno hinterland which have fine old Turkish houses for restoration - plus fresh air and a sea view!