For the sake of directions in this walkthrough when I mention north, south, east or west I'm referencing the circular mini map. North would be the one arrow on the mini map that is more prominent.
Immediately at take off turn approximately 45 degrees to the right and you'll see a bright blue light from a welder on the top of a construction building. Pedro is there.
Go to the very first waypoint of this mission. There is a fenced in building on top of a small hill. The crate is just to left of that building in a small valley between hills.
When you start the mission you need to destroy an outpost. Destroy it. Immediately after the objective is to destroy the factory. Fly straight ahead to the south east side of the map. The crate is behind a low brick warehouse with two big pipes coming out of both sides. This is part of one of the factories you need to destroy.
After entering the cave you'll be piloting a drone. Immediately upon entering the cave turn around 180 degrees and fly down the tunnel. Pedro is there at the very end.
After returning to where you started there is a small room directly to your right. The crate is in there on the right hand side of the room.
After the sniping section you'll be tasked with clearing the hideout. Find the lighthouse on the coast and follow the coast around so the water is to your left. As you round the corner there is a fenced in barn with Pedro standing in the middle of the fenced in area. This is on the north end of the island.
Continue following the coast around to the east side of island until you see a small fire and a raft on the shore. The crate is right there near the fire.
If you continue to follow the coast from there you'll come upon a small fortress wall. The crate is inside these walls. This is on the southeastern side of the island.
When tasked with destroying the radar station fly northeast from the station, across the river right to a mountain that is in the center of that strip of land. Pedro is right on top of the mountain. Do this before you completely destroy the radar station because if you do you're immediately taken to a section where you don't have control of you chopper. I'm sure you can find it later in the mission but its right near where you are for the radar station so grab him now.
From Pedro fly just a short way directly north. Near an intersection on the road that runs down the center of the island is a crate. If you already have Pedro this area is just southwest from the two bridges you destroy during the boat chase.
Immediately after regaining control of the copter after destroying the coca fields the crate is right in this area. It's at the base of a mountain, kind of near the waters edge in a small clearing. You don't need to fly far at all from where the game gives you control of the copter again. If you just spin to the right you should see it.
On the south side of map, behind the really tall oil tower and near some power lines is a crate behind some houses. Very near the maps edge.
Go to the southeast edge of the map. This is the end of the map near the flight control tower. You'll see a small fire and a car. Pedro is in this area.
You'll need to find a vehicle. From where the dump tuck is parked a crate is just to the southeast of there. It is in a group of three piles of purple and blue shipping containers kind of near a crane and a building with a small smokestack.
From the base you start at there is a large mountain directly to the east. Fly over this mountain and the crate is at its base near a road.
From the first outpost you need to eliminate fly directly north. Pedro is standing in a small fenced in area with a small house near it.
In that same outpost there is a radar station atop a hill in the southern part of the outpost. From that radar station fly south-southwest. There is a crate amongst some hills there.
Well I get up in the morning and I get my brief. I go out and stare at the world in complete disbelief. It's not righteous indignation that makes me complain. It's the fact that I always have to explain. - Van Morrison