First to the question hard top on or off? It's your car, I would think you would know how you prefer to drive the car and that is what you should do. Somebody earlier suggested that you not leave the top folded in the down position for long term storage. I would agree with that. Also, if you have air conditioning I find that my AC is more effective with the hard top on then with the soft top up.
On the second matching number issue.... There can be no definitive answer as to added value in all cases. if a potential buyer cares about that particular issue then sure there is value but I would think most buyers are interested in the condition of the car 1st. There are all types of owners out there that enjoy their cars. Are all the production paint spots correct? Does the car look exactly as it did when it rolled out of the factory? If that is your goal in owning one, go for it and enjoy the journey getting there (or paying the price for one that matches your goals.) If you get enjoyment from owning and driving one of these cars, even if the "experts" might have a field day pointing out minor inconsistencies vs. "original", smile and let them have their fun. After all, at the end of the day it is your car to enjoy, not somebody else's.
I knew a Corvette expert who spent countless hours on a nut and bolt restoration of a 66 Corvette. After wining a national concours competition he rolled the car back into it's trailer and he stored it for several years when he later gave it to his daughter as a present for her sixteenth birthday. He smiled when he told me that story and said that the satisfaction of winning the competition could not hold a candle to the smile on his daughter's face.
Remember, you decide what makes you happy. Not what someone else thinks.
Norm