In Cusco try the Mercado San Pedro. All locals. Brush up on your Spanish. The food stalls are in the back.
Beef tendon with eggs and chayote
For local cuisine Pachapapa was very good:
Front and center: Cuy (just to say you did)
Upper right: Beef seco (excellent and highly recommended)
Upper left: pork stew in beer (okay)
Make sure you go to the Sacred Valley and Ollantaytambo.