Are you planning on staying IN San Jose? I lived there for 6 weeks one summer doing a study abroad. Be warned that driving there is more akin to driving in Rome or Egypt than US or Canada: lanes mean nothing, speed limits mean less, and there are 6 lane traffic circles that make less than zero sense to anyone but a local. There is a reason they don't get licenses until 18 there, and it's a very hard test to pass. Oh, and since the rains monsoon down there, their "gutters" are 3 feet deep or more on the sides of the roads. You can easily get around the city and the country on bus instead, and honestly, you'll have a lot of fun that way I think. (Well- West coast and Northern regions really accessible by bus. East coast less so, but as pointed out, you can get yourself into some trouble there and unless you like 'roughing it' a bit more, there isn't as much accessible).
As for the city itself: read up on local hazards, like "pirata" cabs (unauthorized cabbies). There isn't a lot of violent crime, but around heavily traveled areas like the coca cola bus terminal there can be a lot of petty theft- grab and run on bag or cameras, pickpocketing, etc. This is like any big international city, so I don't want to scare you, just be aware that San Jose itself is very different feeling from other parts of Costa Rica.
I will +1 to Jaco feeling like too much of a tourist trap. Lots of expats getting really smashed in bars and beach vendors. Also +1 to Manuel Antonio being one of the most amazing places ever. There is a hostel named something to do with frogs... don't remember exactly, but it was lovely.
I didn't get sick living down there, even diving right into local foods including street foods. But I've also never gotten food poisoning at home, or in Egypt, so maybe I'm an exception? You can always be safe and only get drinks that have been boiled first (ie, get coffee or tea, or bottled sodas, don't do juice because those are often thinned with unboiled water).