I dont know of any birders hotel in San Jose but a lot go to the
Bougainvilla. It has earned a reputation as the place for birders to stay in the Central Valley because tour groups use it. Birding is fair on the grounds and it is secure but its also expensive and not that close to the airport.
Orquideas Inn is cheaper, closer to the airport, and has good habitat.
Zamora Estate is rather expensive but also fairly close to the airport and has the best habitat- ponds, woodlands, and scrubby fields.
Rincon has great birding!
Cerro Lodge and Villa Lapas are a similar distance to Carara and yes you would need a ride. In my experience, taxis charge more from Villa Lapas. Both places are great for birding but more species can be seen at Cerro that probably wont be seen in the park.
If you take a shuttle, ask to be dropped at the crocodile bridge and arrange for the hotel to pick you up there. This is much closer than Jaco.
Here is a link to
bus schedules throughout the country. You may have to go to San Isidro to reach San Vito although you can also get there from Ciudad Neily.
You might pick up a few new birds at Los Cusingos but in general the avifauna is pretty similar to that of Wilson Botanical garden.
I noticed that you didnt have any site on your route for high elevation species. A high percentage of those are endemics and include things like Resplendent Quetzal and Black Guan so you might want to consider staying at Bosque Tolomuco (as was mentioned), at
Paraiso de Quetzales, or La Georgina (a roadside diner with cheap, basic rooms, a couple of cabins, and excellent, rather cold, high elevation forest. There are also more expensive places to stay in the Savegre valley although its not easy getting down there without your own transportation. El Toucanet is also excellent but ditto on getting there without your own vehicle.