I mentioned him earlier, but I highly recommend Ruben Palomino (email@example.com
), a travel agent to help book travel in Peru. He's not kiting related, but he was great about booking all sorts of night buses and made sure people met you in distant cities to make sure you got places safely. It sounds like you would feel better if you used a local travel agent like him to help you.
Otherwise, I think it's plausible to fly into Lima (I would stay in Miraflores), and use your hotel to help you book an overnight bus to Mancora. I agree that you should go first class-- the one time we took the local cheap bus, my laptop was stolen out of our carry on bag under the seat. You should put your belongings within eyes view.
Don't know what is going on with the political situation in Ecuador, but the Galapagos is a natural preserve of islands some thousand+ miles offshore. Logically, unless you think the Ecuador airports could close, you should definitely go and not worry about it. I haven't been, but I've heard that it exceeds all expectations. Unless you know of something specific, it sounds like it's like worrying about LA riots when you are taking a trip to Hawaii... i.e. probably not that relevant.
Sounds like an amazing honeymoon and you should definitely enjoy both parts!