1) The best way to arrange the rafting is to just go with one of the major rafting tour organizers:
Rios Tropicales (the largest)
http://www.riostropicales.com/packages.php?page_id=87Aventuras Naturales
http://www.toenjoynature.com/ONEDAY/INDEX.HTMLExploradores
https://www.exploradoresoutdoors.com/pacuare-rafting.htmlBTW, if you can stand to spend a night away from SJ, I suggest you take one of the day tours to Arenal (sightseeing along the way there), stay overnight (enjoying the hot springs included with the day tour - hotel extra of course, but you'd have that expense in SJ as well) and use Exploradores to return to SJ for free (enjoying their Pacuare trip during the day). The drive out to the Pacuare is pretty long and of course to Arenal it is even further, but by combining these activities you get to enjoy 2 really great trips (hotsprings and rafting) PLUS you wind up with a lot less total drive time AND at little if any extra cost than if you did each tour independently.
2) I don't know of any combo DAY tours that include rafting on the PACUARE and a ZipLine but there is:
http://www.costa-rica-tour.net/tours/super_combo.php that combines a 10 cable zipline tour with rafting on class II-III SARAPIQUI River and
http://www.riostropicales.com/packages.php?page_id=53 which a TWO day rafting trip where you can participate in the zip-line canopy tour they have at their lodge. Of course if you're gonna do something like that, you could as easily (and more cheaply) do a rafting trip one day with a seperate zip line tour the next and be able to spend the night in SJ rather than somewhere out in the rainforest.