Hey, I'm doing a similar itinerary except starting in Puerto Viejo. From San Juan it's relatively easy. See this site for directions www.tortuguerovillage.com/traveloptions.htm, you'll be taking the public buses and then a boat at the connection point, it's pretty cheap! Like $7-10. Then to Arenal, which is where I'm going after also, you can take a shuttle. See this site though I found info online from a hotel (probably outdated) that said they would do it for $35. I forget which one, shop around on the site, all the hotels/hostels/lodges are listed.
There is one company that said they would add on to a package for a cost of $30 transport to San Jose that also included lunch and a hike and another canal tour. Might be worth looking into even though it means tracking back, I haven't decided yet myself. But there are plenty of shuttles if a little expensive. Otherwise you need to track back though I will report if I find any options.