Did you address water issues with a Steripen, filter, or chemical treatment?
I tried to be 100% with the Steripen everywhere in Perú, and had good results with it. I used it even on bottled water since the world over bottled water meets local standards. I would pour the bottled water into a Nalgene bottle and zap it with the Steripen.
The only time I suffered the consequences of the water was in Cuzco, when I absent mindedly drank two cups of coca tea in the hotel lobby.
I'm really paying attention to what happened to you with altitude. Just another comment on the altitude there....for me, I found the adjustment was required going down as well as up. No stomach problems the whole trip in Perú, but I found myself wandering around like a zombie in Lima, at sea level, waiting to fly home. For days after getting home, I still found myself adjusting to the altitude changes.
Facinating story, keep it coming...