I travel to Peru end of July and have 4 weeks to travel around. Fly into and out of Lima and will be travelling with my girlfriend. Have done a bit or research and was thinkng of viisting arequipa, puno/lake titicaca, cusco (and machu picchu) and also spend some time in the amazon (iquetos or peorto maldonado?) Would like to experience a traditional ayahusaca ceremony at one of these places? Not an expert on this part of the world! Am I missing anywhere major here? Would it be worth making the trip over to La Paz? Any advice on suggested routes, timespans, places to stay etc much appreciated!
Almost two years ago I spent 6 weeks in Peru volunteering/travelling and did pretty much everything on your list. Was based in the Sacred Valley Monday-Thursday teaching English and spent weekends travelling. Did Machu Picchu on one weekend, Lake Titicaca on another, spent a week at an Eco-lodge in Puerto Maldonado and then a week in Arequipa/Lima.
If they are the only places you're keen on seeing, the best route would probably be to fly/bus into Cuzco (I did both - flight took about an hour and the bus journey was supposed to take 22hours but in fact ended up being more like 28!), spend a day or two in Cuzco to get used to the altitude, then spend a few days around the Sacred Valley. Make sure you don't miss the Pisac market, Ollantaytambo ruins, Sacsayhuaman etc.
There are plenty of tour companies in Cuzco that will sort out your whole Machu Picchu experience - all travel, accommodation, guide etc. A 2 day visit tends to be enough, as Aguas Calientes is more or less an overpriced tourist trap.
Once you've done the whole Cuzco/S.V thing, you can take several buses and make your way back to Lima in a big loop.
Cuzco - Puno
Puno - Arequipa
Arequipa - Lima
Once you're in Lima you can sort out a stay at Puerto Maldonado/Iquitos. It's easier to fly into both, as Iquitos is virtually inaccessible via land, and the road to Puerto Maldonado is quite treacherous.
If you have time after it all, make sure you head north to Trujillo! It's only a couple hours from Lima and is absolutely beautiful!