Getting to the Ruins at El Peru/Waká
(Wikitravel would call this a stub).
This is a three day trip that you can book from any agency in Flores or Santa Elena, but it looks like you could do it yourself if you have a tent, other camping equipment and water filtration and you bring your own food.
There are buses to and from Paso Caballos from the Santa Elena bus station, but I don't know the times or the frequency. I didn't see them or it listed. You would need to find out this information by going to the relevant Santa Elena bus kiosk and ask.
In theory you could arrange a boat from town, but because our guide showed me a trail that he said would take three hours to hike from town, my impression is that even mediocre hikers would not need one.
Like most Guatemalan jungle ruins, it has a place where you are welcome to cook and heat water. Because of the 22 man military presence, it is larger than most and quite safe. There are elevated places where you can put a tent and if there has been rain recently, ask where you can shower.
My impression of the three day tour is that unless you like to fish like we did, even with a tour, this would not have to take three days.