I would prefer to start with a common model as a basis for modification. I would never do anything major to a rare model such as a special edition, and definitely not any Cooper or S. If I wanted a modified one I would build it to be mechanically identical from the necessary parts and a normal car. Of course I could not then call it or badge it as a Cooper. It would just be my creation. Nothing wrong with replicas as long as they are not fraudulent. Likewise for the interior, an exotic one is priceless. I would fit normal seats, or aftermarket items, for regular use, instead of wearing out the fancy ones, just putting it back to standard for shows.
I would take that view with anything old and rare. Keep it original, but if necessary make temporary substitution for irreplaceable parts so it can be used, and then returned to its original state when passed on to someone else. It may even take its place in a museum one day.
But as I said, with common models that are not needed to preserve history, do what you will, and do it well. Satisfy your creative instinct. Make your ideal car. Have fun!
Door cards and rear shelf are the original ones re-covered and bits of the door furniture taken off. I've also got under dash LED's and just loads of tat to make it personal to me, can easy put it back to original. Purists aren't a fan but Taters gonna tate. 
