I'm planning some of the same routes and from my perspective the time frames are doable (barring bad luck!). I find it helpful to zoom google maps to a section I'm interested in, apply the photos layer, and find good points of interest (and sometimes paved vs. gravel).
Uyuni Salt Flats - Cusco - Lima: I've got a different time frame so not much help here (avoid rainy season). Unless you take shortest route I doubt 1 week fits Machu Picchu (been there, worth it). If you like the looks of Colca Canyon, probably drop to Arequipa first, then on to Puno (Lake Titicaca) and up to Cusco. Head to Nazca (lines), Ica (sand boarding/oasis), and on to Lima. If you don't have time to see Macchu Picchu, see the rideable remote sites (Moray, Salineras).
Lima - Quito: I'm almost done routing (lodging needs some work)
https://maps.google.com/maps/ms?msid...39b1eca7&msa=0
Here's estimated daily mileage, and keypoints to research:
Day 1, 200 Miles, 5 hours
Lima, Sanctuaria Nacional Huayllay, Cerro De Pasco (ugly copper pit town), on to camp. This is to see the Huayllay rock garden but if you’re not interested (another one available later in route) then go directly to Huaraz from Lima via Coastal 1N (straight) and 14A (twisties).
Day 2, 200 miles, 5 hours
Head to Huaraz with sights of Waywash Mountains (Amazon watershed).
Day 3, 65 miles, 1 hour 30 minutes
Hike Huascaran National Park: Churup Glacial Lagoon or Palcacocha Lagoon. Pre-Incan ruin Wilcahuain. Continue on to Yungay for the night (read on Yungay tragedy).
Day 4, 160 miles, 3 hours 30 minutes
Head to coastal city of Trujillo. Ruins of Chan Chan, Huaca del Sol y la Luna Temple. Ceviche Cuisine Birthplace.
Day 5, 160 miles, 3 hours 30 minutes
Head to Cajamarca (Incan emperor Atahualpa captured here). Route goes through Coto de Caza Sunchubamba a verdant protected area. Llacanora Cascades (1 mile hike). Cumbe Mayo 1500 BC aqueduct, petroglyphs, rock garden. Cajamarca Banos del Inca.
Day 6, 200 miles, 5 hours 30 minutes
Head to Chacahpoyas. The Cloud People, Kuelap Fortress, Los Pinchudos.
Day 7, 85 miles, 2 hours
Hike to Gocta Falls (5th or so, tallest in the world). Ride to Cajaruro.
Day 8, 180 Miles, 4 hours 30 minutes
Head to La Balsa, the Ecuadorian Bordertown.
Day 9, 120 miles, 5 hours 30 minutes
Head to Loja, Ecuador (or Vilcabamba & Mandango, the Sleeping Inca Rock Formation)
10 through 13, 400 miles 8 hours 44 minutes to Quito
Haven’t made this route yet, but seems more than doable.
Hopefully someone who's done these routes can weigh in. Good luck!