Alon,
Sounds like you have some of the main highlights picked out for yourself in Peru – all those places you mentioned are well worth visiting. I was in Huaraz last November for several weeks and hit fantastic weather. Even at 2800 meters it was surprisingly warm during the day. There can be some rain that time of year but I don’t think its generally that bad.
Iquitos is warm all year round but never too hot and definetely not too cold even at night. I would expect some rain, but not as much as you would see during May through August. I don’t remember too much rain when I was there – maybe brief but heavy showers.
Since Iquitos is landlocked you will have to fly out of Lima on a non stop flight – I think it takes about 90 minutes or slightly less. LAN Peru is the best option.
So you will have to take a bus to Huaras as there is no commercial air service and then you will have to come back to Lima. Then you might want to go to either Iquitos and return to Lima or start the other part of your trip and then come back to Lima and do Iquitos towards the end.
You can take a bus to Cuzco from Lima but its incredibly long and becomes very windy when in the Andes. Depending on your budget, I would recommend flying to Cuzco from Lima and then taking a bus down to Titicaca and then down to Arequipa and flying back from Arequipa. Or if you don’t mind taking buses – try for overnight sleepers (saves hotel room and day time hours) – I’ve taken a bus from Ilo (a few hours from Arequipa in the south) back to Lima – it was like 18 hours. Long bus rides are crazy, but doable depending on how well you travel, budget and timeline.
I’ll pass by your comments/questions to some of my Peruvian friends.
Have a great trip!!
Regards,
Dave