Your VWP comes under the ESTA program and is valid for a two year period. You don't need to reapply for anything during this time, and indeed you can use it multiple times, and they email you when it's expiring.
However, there is, as you've acknowledged, the 90 day rule. Even more frustratingly, as many have found out, you cannot reset it by simply going to Canada or Mexico.
Yes, it will be reset if you go to Costa Rica or Guatemala. However, as with any entrance into the USA, it's up to the border agent as to whether or not you are permitted to enter.
Such a trip will raise a potential flag as 'possible border run', which some might do if they're working under the table in the US but want to maintain a visa. So to placate them, and assuage their concerns, you'll want to provide evidence that you're only staying for two more months. Itinerary, bookings, train/bus tickets if you have them, and definitely your flight out of the US at the end of the two months.