Hi! I will respond in parts, too much information to handle LOL
I will suggest you to buy your air tickets right know, it is cheaper when you buy 2 - 1 months before your actual travel. The cheapest will be the local airlines, LC Peru and Star Peru. And the super duper cheapest of all is Peruvian Airlines, who doesn't make any difference between foreigners and locals when it comes to fares, plus they don't charge you for changes... For example a round trip Lima-Cusco always is like $100... In other airlines it can be high as $400 in economy! And Peruvian has flights to all your destinations you list on your post...
For the bus tickets things are more flexible, there are a lot of buslines and very nice terminals, at least in the case of the one I used here in Lima, you can even check their website http://granterminalterrestre.com/destinos
I have experienced the service of TEPSA bus, and It was very good, I've also heard very good comments about CIVA, they have one of the best services.
Never done it before
But I know that in the Miraflores area there are some places you can do paragliding! The best place to get more information is TripAdvisor I guess... If I get more info I will post it here.
PHARMACY: Here are called Farmacias or Boticas
As you should know, the prices vary from pill to pill
I don't know if they're cheaper here but I know that you can buy some really good quality generic drugs for a cheap cheap price, there are brand names too if you like. There are a lot of pharmacies everywhere...
Well, all depends on the budget you have, but you must know this, Lima can be super expensive or super cheap! There are options for everyone, Let me know what kind of stuff you would like to do in Lima and I will tell you the best accommodation for your choice. In Cusco I've stayed in a place really really close to Plaza de Armas, where all the action happens
It is not luxurious but it is cheap and very convenient.
I'm here to help. Have a nice one.