Hi Korshmar, good questions!
We haven’t done the Rio Frio tour yet but have heard that it is an excellent river to see birds and other wildlife. We’re not experts on that river but our friends over at Costa Rica Birding Tours have a great article about it. It looks like you might better visiting during the dry season, at least for birds. In June the waters could be high and less birds and animals would be along the banks.
Similarly, the Pacuare River could also be high in June (depending on rainfall) and a little intense for rafting. If that’s the case you might get sent out on the nearby Pejibaye River. This river would be a lot more manageable when the waters are high but still a lot of fun. Alternatively some companies also make a stop on the Sarapiqui River on the way between La Fortuna and Puerto Viejo (de Talamanca). One that we know of is Gecko Tours. We recently rafted the Sarapiqui River with the Outward Bound organization and really liked it. You can read more about our experience here to see if it might be a good fit.
Hope this helps with your planning. Thank you for the kind words about our book, we’d love it if you’d take a second and leave us a short review on Amazon to help spread the word!
-Matt & Jenn