Lima is a big city, and I personally do not enjoy big cities in Peru or any other country when traveling by motorcycle.
One of the best experiences I have ever enjoyed was riding from Cusco through the Sacred Valley to Machu Picchu! The ride was only surpassed by the hospitality of the villagers. I hope you have the opportunity to travel through the Sacred Valley region, and if you do feel free to PM and I will be happy to provide route information.
All the Best,