The answer is yes to all your questions. The coffee tours, raft trips and rainforest/wildlife all make excellent trips and the DR travel desk does a good job helping you arrange them.
Here are a few other options you didn't mention.
1) The All-in-one or the 4-in-1 tour (its been called by various names) is a great option for someone in for just a quick trip for the first time. It covers Poas Volcano, a coffee farm, La Paz Waterfall Park (with its rainforest trails, hummingbird gallery and butterfly garden), Sarapiqui River boat trip and a late return through Braulio Carillo National Park. Warning, it is a fast paced and very long day.
2) Canopy tours are another highly popular option. Be forewarned though: they're really much more of an adrenaline rush than a real ecotour and the airtime itself only lasts for an hour or two.
3) A driving tour of the eastern valley is yet another good option which includes Irazu volcano and Cartago (half day) or adds Lankester Gardens and/or Orosi Valley for the full day version.
4) A lot of guys rave about the Tortuga Catamaran Tour which involves a drive down to the coast and a sail cruise out to an island in the gulf of Nicoya.
5) I've down a mountain bike tour (mostly downhill) includes an utterly thrilling flight down one of the volcanos, but its definitely not for the faint of heart.
This covers most of the better tours. There are others like the Butterfly Farm, Aerial Tram, City Tour (not recommended), Western Villages (Saarchi, Grecia, Alajuela) and I'm sure a few I've forgotten or failed to mention. And those are just the ones that are conveniently done from SJ. If you came back to CR later, there are even more to be taken that are further afield from SJ. Do a search on those listed above to find out more info.
Still hopelessly confused? Don't worry, you'll probably want to come back to CR and you can always see what ever you miss on later trips. That is part of the beauty of CR that it has so much repeat value. Going with your initial picks are probably the best way to go unless you opt for the all-in one which combines the coffee tour and wildlife allowing you to select one additional tour. All-in-1 Friday, Raft Saturday (or vice versa), and an easy half day Irazu/Cartago Sunday that gets you back in time for an afternoon MP and the evening Party sounds like the best recipe to me. If thats too busy, do Cafe Britt instead of the all-in-1, you'll get back early enough for a daytime session and will get wildlife during your raft trip and your volcano on Sunday.