RE: travel Lima-Cuzco-Puerto Maldonado
It could take you a long time by bus because highway system in Peru is unreliable and unpredictable. We encountered meat tax protests where villagers threw large rocks onto the highway to block traffic. We were held for a few hours (in a long line of vehicles) when the villagers finally decided to move the rocks. Protests are regular affairs.
Best way to go is by air. It's a short flight from Lima to Cusco. The thing is weather can be unpredictable in the Andes. We were held up in Lima airport for a few hours to wait for weather to clear up.
It's definitely possible to do all in 16 days. Earlier this year, I went from Lima to Puerto Maldonado by flight, Puerto Maldonado to Cusco by flight, Cusco to Ollantaytambo by bus, then Inca Trail, Agua Caliente to Ollantaytambo by train, Ollantaytambo to Puno by bus. I didn't do Huaraz, so can't help you there.
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