Sorry for missing this one.
To be honest, i usually try to avoid mixing MVC and Kentico, it may be a better option to keep the MVC as a virtual directory on the site. To my knowledge, although MVC support is growing, you still can't do portal editing in MVC, or minimal, plus there's the issue of needing a hard coded master page.
I've found ways to mimic MVC like behavior using Kentico's portal, but it may or may not be applicable. For example i converted the MVC View classes into data sources so i could use repeaters to display. I used Custom Tables and Forms and loaded data into them and then grabbed it out so they can edit form data using Kentico's forms engine, etc.
If you need more details, i can provide! Another option lastly is if you still want to 'integrate' i would see if you can duplicate the header / footer content from the master page and import it dynamically to the MVC header and footer, maybe through the .net HTMLAgilityPack to grab the header/footer and apply them to literals... all depends on the situation, pros and cons to each.