Another issue I can see apart from those already raised are that there's no direct Rio-Lima flight, so that adds another segment (you need to fly via Santiago to get there). If your itenary is flexible you could go from Sao Paulo to Buenos Aires on BA first, and then Buenos Aires-Lima, and back to Santiago.
As for the security on buses, I can't speak for other countries in South America, but in Brazil it seemed fine for me. I couldn't speak any more Spanish or Portuguese than what I plucked out of the phrase books, but didn't experience any problems buying tickets. I was pleasantly surprised by the quality of the bus stations in Brazil too, especially compared to those in S-E Asia for instance (and I'd definitely rate the bus terminal in Sao Paulo as better than many airports I've been to even in Europe and the US). That said, I'm an above average sized guy, and so your mileage may vary in regards to safety, but if you keep in mind the points Darren has listed you should steer clear of most trouble.