My wife and I are just starting to plan a 16 day trip to Peru - Cusco, Jungle Lodge, Inca Trail & Machu Picchu. Because of work we can only go for 16 days in May or November. Would there be much difference in weather? Any other differences between those two months?

You might start running into some rain by November. Between the two, I'd choose May. You'd have decent weather, but the June-August crowds won't yet have begun to arrive.

I am going in March which should make it summer time weather.

You will still have good weather in May.

Percy

It's better to think of it as "rainy" and "dry" seasons instead of "summer" and "winter" months in that part of Peru. You'll find the best weather (least rain) in what would be the winter months (June-August), but that means more crowds too. May is an ideal time.

If you are concerned about rain, definitely go in May. It is also much greener in the mountains still and really pretty. With 16 days, you can have a very nice trip if just doing the jungle and the Cusco/Machu Picchu area. My vote is for May. i am in Peru all the time as I have a custom travel service and also lived there for many years. So, I add in my vote for May.