Just got back from a successful full million mile run. Can't thank everyone on this board enough, especially the early travelers, for posting all the info that made planning and taking the trip so easy. Luck was also on my side.
I'll try not to repeat what everyone else has already posted, but hope some of my experiences can be helpful.
Did the trip in 5 days, but could have been done in 4 if I didn't take an extra day to do Machu Picchu.
My route:
US BOS/CLT/FLL
Avis FLL
TA MIA/MGA (for Nica)
CM MGA/GUA
Radisson GUA
GU GUA/SAL
TA SAL/SJO
LR SJO/UIO
Hilton UIO
VX UIO/LIM (for SAETA)
TA LIM/CUZ (for Taca Peru)
Hotel Monestario CUZ
TJ CUZ/LIM (didn't count for bonus)
Holiday Inn LIM
VH LIM/GYE
AV GYE/BOG
VX BOG/MIA
US MIA/BOS
Every flight, except TJ, operated on time or early. I was in business class on all flights where available. Equipment and service on all carriers except AV was well above average. VX coach service beats business/first class service on many other airlines.
I'd recommend all of the hotels eventhough I didn't some of them use them for more than a shower and couple of hours of sleep.
At every immigration counter I started every conversation with Transito and it allowed me to avoid departure taxes at most airports. I had to pay it in Peru because of the overnight, and had to pay the minor domestic departure taxes twice.
Some of the airline agents at check-in counters tried to be "helpful" by switching me to non-stop flights so I wouldn't have to make connections. They didn't understand why "loco" Americans want to travel this way.
I followed everyone's advice for getting through I&C and staying in transit. The only time I didn't was in LIM - and I was sorry. Instead of being in the international transit area for 6 hours overnight, I ended up in the domestic area with blaring TV's, and maintenance staff moving each chair I tried to sleep on so they could clean the floor. If you do this connection, stay in International transit until at least 4am when the Taca Peru check-in counter opens.
Although you are constantly reminded to allow at least 2 hours for check-in, if you have a biz class ticket, an hour is enough, except for BOG. Some of the flights left up to 30 min early, so don't cut it too close.
The helicopter from CUZ to Machu Picchu & back is a spectacular 25 min flight through the mountains. The flight attendant provides lots of commentary and many photo ops out the helicopter windows. You can book the flight directly with Heli Cusco at +51-84-227283 for US$170 round-trip. If you book it through a tour operator it becomes about $250. Flight leaves CUZ at 8:30am and leaves Aguas Calientes at 3:00pm. Tour operators are also trying to sell the bus from Aguas Calientes to/from Machu Picchu and Machu Pacchu entry for $30-$50. The bus ticket is $6 and entry is $10. Lots of english speaking guides for hire too.
The last flight from CUZ to LIM is the 12:30pm TJ flight. It was only 30 min late, but locals told me sometimes it doesn't run. Lan Peru has a 12:25 flight that was booked full, but had lots of empty seats. I would double book so you don't get stuck there for an extra day.
Great knowledgable english speaking guide in Lima is Floriano Maguina - Tel: 5534026 or 9014425 (cell). Did a great city tour and the Museo de Oro in 5 hours.
I had an $85 confirmed rate at the Holiday Inn Miraflores. At check-in they wouldn't take a Prioity Pass or Latin Pass number for a rate lower than $109.
Had a lot of trouble getting my LatinPass number onto my US Air flights. The airport agents couldn't get it to happen, told me I had to call the Dividend Miles Service Center before the end of the day I took the flight. Called them between flights and spoke to a few people who said it couldn't be done, then finally to a supervisor who said she knew how to do it and would enter my number. It still didn't appear on my boarding passes, so we'll see if it posts.
After making copies, I took the originals of all of my boarding passes, ticket receipts, hotel bills and car rental bill to LatinPass on my return to Miami. They stamped a receipt for me and told me they wait 6 weeks to see if they post automatically from each carrier and partner. If not, then they put it in.
Now I wait to see when eveything posts and hope this part is as easy as taking the run.