well you can get to cusco by plane or bus, but I think that lima is very far from cusco so I think the best options it's what my brother (he went to peru last year) did, he went from lima to Pisco, then, Arequipa, then puno and then cusco. he travel by bus and he go to all that cities that I really like when I saw the photos, he went by his own with his friends but to cusco they take a machu picchu tour because of the popular of that place it is a little difficult to find tours or that the same day.
well good luck.
