Smart Daughter!!! CR is way better than 95% of cruises IMHO.
I've done what you are proposing with my brother who lived in Costa-Rica for a few years and I have returned many times (actually be there in a few weeks for xmas). First, not sure if I would do the bus thing. You can esaily rent a small SUV and drive around.
You can kinda do a loop and get to see the most in 10 days. Here is what I would do.
-Fly into Liberia, rent a car and drive to Arenal Volcano, spend a couple of days there seeing the volcano, hot springs, swiming in the big water falls, etc. There is lots of good places to stay and tourist info. Note that the volcano itself can be under cloud cover for days
-Next onto Monte Verde national park (1/2 day drive). You can easily spend 3 days there visiting the sites like the rain forest, cloud forest, zip lining, etc. Lots of good places to stay along with great restaurants. Be sure to dress for it as it is cool and rains a lot (hence the term Rain Forest).
-Then to the Pacific coast. If you are not into crowds, I would skip Jaco & Tamarindo and go to Nosara Beach and rent a house for a few days. Rent one in the hills overlooking the ocean, not close to the beach. No bugs, no air conditioning & great views and spend a few days Great safe beach, not many tourists, good restaurants. It's a little hard to get to (long dirt road drive of about 45 minutes), but well worth it! This is a good site for house rentals in Nosara Vacation Rentals in Nosara, Costa Rica:
Have a great trip!