Rio De Janeiro to Lima overland

Rio - Sao Paulo - Campo Grande - Corumba - Santa Cruz - La Paz - Puno - Cusco - Arequipa - Lima.
The first four are in Brazil, the middle two are in Bolivia and the last four are in Peru; get yourself a guidebook.

Suggested itinerary:
Rio --> Iguazu (Arg side) --> Asuncion --> Salta --> Tupiza --> Uyuni --> Potosi --> Sucre --> La Paz --> Puno --> Arequipa --> Cuzco --> Pisco --> Lima.
You'd need about 3 months for that trip, at normal pace, with local tours included.

Should I go through Bolivia?

Yes, don't hesitate about that.
Busses are available everywhere and are the most popular way of travelling in South America.

I disagree, bus travel is for the effete.

The proper thing to do for a strapping young lad wanting his gap filled over the course of a year is to go around the Horn, before the mast, as a cabin boy. Ply your passage son! It will be a salty adventure where you'll no doubt make life long friends and learn new skills. If nothing else it will set you up for a career in banking or politics.

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