Is Sept to Jan enough time?

There is a Paraguayan Consulate in Puerto Iguazú; you might consider calling them a little ahead to make sure they will be able to issue your visas.
You are coming from Australia, right? Brazilian tourist visas usually must be used for the first time within 90 days of their issuing date. Be sure to enter Brazil within this deadline, or otherwise you might find yourself in the need of having another Brazilian visa issued in your passport.
It is possible to go from Chile to Bolivia, from Bolivia to Chile, from Argentina to Bolivia, from Bolivia to Argentina, from Argentina to Chile and from Chile to Argentina. Up to you. The place to leave aside if you don't have enough time is San Pedro de Atacama. The Salar de Uyuni in Bolivia is a must, and you can get there either after visiting the Quebrada de Humahuaca north of Salta or after checking San Pedro.
Just stop in Manaus if you want to recover from travelling too much by boat or take a jungle tour from there - but perhaps you might've already done a jungle tour by then, either in Rurrenabaque in Bolivia, around Manu Park in Peru or even from Iquitos. Then skip Manaus, add a couple more days to Santarém and enjoy the unusual and superb river beaches in Alter do Chão, a village nearby in the east bank of Tapajós river.
Keep your couple of days in Belém. The city is indeed very interesting and a cultural hub in the Brazilian Amazon - and way more enjoyable than Manaus.
It is unlikely you'll find Lençois Maranhenses completely dry. This will happen only if a severe draught affects the area. I've been there once in a month of February and the lagoons were still pretty full. I've read a number of reviews stating December is actually a good season to go there. Do go. It's wonderful beyond imagination!
High tourist season in Brazil usually begins in mid-December and lasts until carnaval period. Prices are likely to rise during this period, but appalling impossibility of finding accomodation is more likely to happen a few days after Christmas up to New Year's, and then again in carnaval. But since December-March is a period of summer vacations in Brazil, some places tend to get packed easily. Belém won't pose any problems in this sense, since it is still relatively a "kept secret" in terms of mass tourism. Salvador doesn't really stand behind Rio in this sense: better if you can book accomodation ahead - unless you are travelling on a higher budget and don't mind putting up in ritzier hotels. São Luís and Lençois Maranhenses are less frenzied than Salvador and places around in Bahia. As you are visiting the area before New Year's, I bet you won't have that much trouble finding a place to stay. However, booking a little in advance is advisable.
Luckily for you, you have the greatest challenge settled: you have a friend's place to stay in Rio! Just take care to book your flight from Salvador in advance.
For Ilha Grande and Parati: YES, YOU SHOULD EXPECT DIFFICULTY FINDING ACCOMODATION for the first week of January. Since you already know you be around the area, book as much in advance as possible.
Have a nice trip!

Hey thanks for your info, very, very informative.
Regarding the Brazilian visa, we received it in July and notified then that we would be arriving in Brazil in mid October, which is obviously outside 90 days of issue, and nothing is mentioned on the consulate website, but I will contact them just to be certain.

I'm pretty sure a Paraguayan visa can be issued on the same day, but as you suggested, it's probably worth checking before hand.

We were originally interested in San Pedro de Atacama for a couple of reasons, 1. We would like to do a cross of the Andes, and we have heard the pass between Salta and SPA is quite beautiful, and 2. We were interested in the observatory night tour thing.

Of course we will definitely go to Uyuni salt flats, that is a huge highlight for us.

Manaus was going to be just a rest from boat travel, most people say there is not much of interest there so 1 or 2 days only, but thanks for you're recommendation to stay a couple of extra days in Santarem and visit Altar do Chao, I've heard it's a fantastic little spot.

As for accommodation, we should be able to book at least 1 week ahead of each place we want to stay, usually more if we really do some planning.

Bolivia and Peru are countries we really do not want to rush, and given that they will be the be the cheapest of all we can afford to take our time, so I figure if we see that we are running out of time we might just spend a few extra weeks in this area, then fly from Lima (for example) to Rio just after Christmas, then continue with our original itinerary.

From what I've read, you can't get a Paraguay visa at the border, you have to get it beforehand. I'd suggest going to the embassy in BsAs when you land there and get your visas then so there's no visa snafu later on.

#3: getting the visa at a Paraguayan consulate will not be considered a "border visa". But the OP should check that possibility beforehand. I'm very wary about consulates in general, which tend to be quite unpredictable and whimsical in their way of working things out.
OP #2: do recheck your visa status with the Brazilian consulate that issued it in Australia. Don't risk arriving here and being denied entry: the risk exists!
Good luck!

I think it would be much better to go from BA to SAlta and then a flight to Iguazu from Salta and then your way to RIO....
You need at least five days for this area. For Salt and Jujuy province I mean....
Warm regards,

Thanks again for your words of caution regarding the visa issues, I'll definitely be checking up on them.

#5, I've heard the Salta area is fantastic, thanks for the advice.

I've tried calling (also emailed) the Brazilian Consulate in Australia regarding the issue of the visa expiring after 90 days if it is not used however I just got a recorded message saying that they do not answer any queries regarding visa information, and all info is on their website >_<.

I've trawled right through their website and no where does it mention anything about having to use the visa within 90 days of issuance, in fact, it says when applying for a visa, you should apply as early as possible before the date of entering Brazil. I was issued with mine in July, so already it is almost outside 90 days. I just hope they stick with this story when I actually arrive in Brazil. I'm not sure what else I can do to be sure.

http://sistemas.mre.gov.br/kitweb/datafiles/Sydney/en-us/file/Visa%20Information/TOURIST_VISA.pdf

http://www.brazil.org.au/aussie/page.php?id=124

I also came across this in my searches on another website:
"As of January 11, 2010, Brazil is no longer issuing visas that bear "first entry within 90 days from the date of issue" allowing travelers to schedule their trips more freely."