I live in Sao Paulo and just to follow up, I do think it is worth a day of your time, if you are here anyway. Go to the Torre de Banesp or the Teraco Italiano for a view of the city. Both are in the city center and you have a feeling of entering the next century when looking over the endless number of skyscrabers...
I totally agree with most people, that of course you should take buses - no problem you will get by having a small parloer or something like that. Although, please take care at the busstations in the big cities - Rio and SP. Like not asking random persons for information but stick to the buspersonal or security guards. Just use common sense and you'll be fine.
Yes, you can take a direct bus from Sao Sebatian to Paraty. To get to SB from Sao Paulo go to the Tiete bus station (can be reached by metro station). The journey is about 5-6 hours. If you are going to Ilha Bela the bus stops in SB rigth in front of the ferry which is free for pedestrians - so get on it - leaves every half hour. On the other side on Ilha bela, there are buses running up and down the only road that exist there (cost very little). Once you want to go to Paraty, take the ferry back to the mainland and you will have to walk some 500 meters (as far as I remember) to reach the busstation (rodoviario in portuguese) in SB. From there you can take a bus to Paraty (I think it will be some 6-7 hours) and the trips is very pretty as you'll pass the 'litoral norte' which is very beautiful. Hope it helps. Ilha bela is very pretty and Paraty is one of my personal favorites. Take a boat trip there to some of the off-road beaches in the area.
About Foz de Iguacu, yes you can take a bus from SP (16 hours) but if you have the money it migth be better to fly either from SP or Rio. The bustrip is not so exciting (runs through farmland landscape) and is quite long.