About the OWE segments, you get 4 flights in a continent, does not matter if they connect or not. Matters in the continent of origin as you can have only 2 stopovers and if there is an open jaw, that counts as a stopover. Now, the global explorer it does matter since the mileage of the surface sector counts against the mileage limit.

I was in S.America in 1995 so my experiences with the trains that I used may have changed alot since then. Better to drive to the trail head of the inca trail, hike into Machu Pichu. Its not difficult at all. The train was long and swayed a lot. Ok if only riding to the road connection. The train to Puno from Cuzco was a real milk run and adventursome even in 1st class car. Sorry, no ferry/boat between Peru and Bolivia. The bus takes a pontoon ride across the river, but that's it.
The coolest train trip was from La Paz to Arica. It is just a single car train, but you can look out the window the same as the conductor. Scenery is fantastic. It was amazing how the on-board steward make a steak and potato lunch in the back'gallery' There are some works by Gustav Eifel in arica and Tacna(in Peru). Never thought I see French work in S.America.
Lastly, the bus ride to Santiago is different. You have your choice of there buses. One is the usual greyhound. One is like biz class on a plane, and the last has flat sleeper seats (i think 25 passengers). Hope this helps.