The Coke in Costa Rica is better than the Coke in the U.S.A. because, just like Jamaica, it's real sugar in the drink and not high fructose corn syrup. There is a taste difference and real sugar is the real thing.
There are tons of things for you and the Mrs. to do in San Jose and the surronding areas. As an example, and because it seems that you can "afford", I really do urge you to take her to Villa Blanca outside of San Ramon. Here is the web site:
http://www.villablanca-costarica.com/ and get a honeymoon suite. That's only $215 per night. The superior room is only $170. This "joint" is full on five star quality; is private as all get out and you're in the middle of a friggin rain forest in the clouds. There is a spa there, blah, blah, blah. I really enjoy my stays there. It is maybe a 1.5 hour drive to there...tops.
Also, you will be paying a premium for beer at the hotel you're staying at because it is a 5 star place. Really, just call them on the phone and spend a few dimes on the phone. You can get all the prices you need off their menu and know what you're getting into. It's cheap to call Costa Rica 9 times out of 10. I pay less than 6¢ direct dial from my landline. It will really ease your mind to phone them and find out "the details".
As for what to do in San Jose the city itself, if nothing else, go to the Central Market and just wander about. Great place to pick up some trinkets and experience what a regular Tico/Tica does. Coffee to buy....not the same quality as Blue Mountain, but excellent in it's own right; and plenty, plenty more to see. You can cab it to and from the Central Market from the hotel where you're staying. She'll thank you.