Along the Panamericana road the bus service is cheap, good, frequent. But, you won't need it since your schedule is
different.
If I were you, I'll do the following:
Lima - Pucallpa (flight)
Pucallpa - Cuzco (flight) - I do not know if there is direct flight...
Cuzco - Puno (train)
Buses are cheap, but in the Andes it takes a long time to travel. Flights are more or less 80 US dollars pp
and it looks expensive, but when you count bus fares along with the fact that you have to sleep and stay in some
places along the way, it breaks even. It is a question if you want to see and experience more, or to
be fit for destinations that you choose.
Do not miss the train from Cuzco to Puno, since it goes along Peruvian altiplano with beautiful scenery that you'll like.
And - buy the first class tickets.
Advice: altitude sickness can appear, so drink a lot of coca tea. It really helps.
On lake Titicaca be careful - take some cream with 30+ factor, or you'll burn. Water reflects the sun.
If you want to return to Lima from Puno, use bus service to Arequipa, then to Lima, you'll
have many attractive things along the way, like Nazca, Ica (wine cellars) or maybe Islas Ballestas.
Enjoy every minute of it, Mike...
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