My opinion is that you are trying to see way too much in too short a time. You'll be spending most of your vacation on busses. If I recall, the bus from Cusco to Puno is 6 hours. The bus from Puno to Colca Canyon is another 4-5 hours and the bus to Arequipa is 5 hours. So on your last 2 days you'd spend 15 hours on busses.
With only 6 days, I would concentrate on Cusco, MP, Sacred Valley and Lima. Cusco and the Sacred Valley area are beautiful and deserve 4-5 days, which would leave a day for Lima. Plan to go back and see Colca Canyon some other trip when you have time to hike into the canyon or stay at one of the villages nearby for a few days. And Arequipa is also worth a day or so.