ellen: you can check on availability of shuttles by going to [www.shuttlebus.co.cr] and do some bookings on various locations - just don't buy a ticket! this will give you some idea of availability and how early you have to book. you can also check [www.anywherecostarica.com] for shuttles also.
as for the order in which you visit -- it doesn't matter that much, mostly, just what pleases you. some things will make more sense from a travel perspective - for instance, going to tortuguero from arenal makes more sense than going from puerto jimenez but mostly it doesn't matter.
by the way - manuel antonio and corcovado are two completely different things. corcovado for hiking the wilderness kind of thing and manuel antonio for beaches and popular national park. look here - [www.manuelantoniopark.com] and here [www.corcovadoguide.com]
now that you have more information, perhaps you can refine your itinerary and ask for comments on that.

