I found gap to be the most expensive and constricting to my schedule. If you like to do a lot of transferring yourselves and don't want to be stuck to a schedule, I suggest going with Peru Treks. It's a hell of a lot cheaper and it's the same services (as I asked a lot of travels who they went with; even GAPers)
What you'll have to cover is the transport, food, hotel. No biggy
Got back from my trip just about a month ago. Travelled from Peru > Bolivia > Chile in a month and a half. AMAZING!
**Watch out for tons of theft, robberies and everything in between :/