Gordo,
About the planning, I disagree with Grant (sorry Grant), as planning is 1/2 the fun for me. Explore away on Google earth, then program your GPS to see some great places. Yes, once you are down there NOT keeping to a schedule is the smartest way to ride...
Wife and I have done quite a bit of riding in Peru 2-up on an XR650L, and I know the KLR is much more comfortable! You are just about to enter the best time to ride in the central Andes (late May to late October). It IS winter, which there means it is sunny every day and never rains, so you can plan and not be offset by bad weather. When the sun shines (even at 15,000 ft, it is not cold, and sometimes even a little hot. just get to where you are to spend the night by 3:30 PMish as it cools off quickly after that.
I HIGHLY recommend up the center of Peru! Have done it various times. Cuzco-Andahuaylas-Ayacucho-Huancayo-Huanuco-Huaraz-Caraz-Huamachuco-Cajamarca-Chachapoyas-Jaen. Over half of that is paved and the other half is gravel in great condition. You will find gasoline everywhere along the way and hotels/hostels with hot water for under $25/night. The most fantasitic sections are Abancay to Ayacucho and Celendin to Leymebamba (on the Cajamarca to Chachpoyas section).
Keep to a limit of 250km gravel and 400km pavement. Those are full days in Peru, especially 2-up. And up the center is safe-safe-safe. Stay away from the coastal #%$@# Panam and Lima! Boring, boring, boring, and at times dangerous. For your partner's sake, rest up every other day, and you will enjoy yourself.
Been living and riding for 30 years in Peru, so feel free to ask any questions, recommendations, etc.
Cheers, Toby

