Note that I think this walkthrough is not quite perfect and doesn't get all possible points. When I was writing it I ended up with only 978/1000; I have added in the things that I think I missed, but I haven't been able to play through the game again so I am not making any guarantees of perfect scoredom.
The Town of Iquitos
Click the hand on your passport in your inventory to find your immunization card, then hand them both to the customs man. Read the sign that the standing man is holding, and talk to him. Walk onto the beginning of the pier at the bottom right of the screen. After Slaughter leaves, talk to the old man. Walk back up the pier, then go east again. Look at the men talking behind the crates, then click the hand on the crates to climb up and eavesdrop. Talk to the tourist. Trash the piece of paper he litters. Look at the boat and the stream of gasoline pouring from it. Walk up to Gonzalez and talk to him. Click the hand on the cargo net. Go west, then come back east. Walk in front of the crates. Buy the parrot from the peddler. Return west and open the single crate next to the boat. Watch the demonstration of how to use the Ecorder. Go back east and ecord the stream of gasoline coming from the boat, then go back west. Watch the scene.
The Forest Floor
When you regain control of Adam, first ecord one of the otters. Talk to Orpheus twice. Take the amulet from around his neck. Ecord the litter, then clean it up. Ecord the ants on the tree, the forest floor, the roots reaching down into the water, and the bushes. Pick up the leaf next to the dripping sap. Go east. Ecord the tree twice in two different places ("Cecropia tree" and "Buttress"), and the cut log near the campfire. Try to climb the tree. Smear the leaf on yourself and climb the tree again. Continue climbing until you exit at the top of the screen. Talk to all the birds and the sloth, and ecord them. Ecord the orchids and the plant beyond the nest. Climb up to the next branch and try to walk west. Ecord the boa. Climb up to the next screen. Talk to each of the birds and ecord them. (Catching the hummingbird can be a trick - try on the yellow flowers at the left of the screen.) Ecord the red plant between the two birds and the pitcher plants (next to the hoatzin). Climb down to the bottom branch (yellow orchids), then go west. Pick some of the purple flowers the hummingbirds were clustered around. Talk to and ecord the bird at the left. Ecord the vine wrapped around the tree trunk, and the forest canopy. Return east, then up to the top. Step onto the branch with the pitcher plants. Click the purple flowers on yourself, then walk past the hoatzin and tip over one of the far pitcher plants. Climb down and watch the egg hatch. Talk to each of the birds and the sloth again. Climb up and talk to everyone up there, too. Then go back down and walk west on the branch the boa was on. Watch the red lizard - that's the path you'll be taking. Talk to the darter again, then walk on the tree branches in the same way the lizard did, and offscreen to the left.
The Village and Forest Heart
Walk to the end of the branch - it will bend, but not break. Ecord the village and the drum lodged in the tree branch (it looks something like a bird's nest). Try to walk down the branch towards the bottom of the screen. Ecord the jaguar. Walk to the drum and pick it up. After you fall into the mud, ecord the long house and the pig. Take the vine next to the mud pit. Ecord the fruits, then take them as well. Throw a fruit to the pig, then lasso him with the vine and he will drag you out of the mud. Go east. Ecord the hanging cloth and the plot of plants that are growing behind the house. Put the drum on the stand next to the one that's already there. Pick up the beater and figure out the song on the hide. Write it down. Pick up the drum again. Go west, then north. Enter the "doorway" into the tree that's closest to you. Put the drum on the stand and play the melody again. After the vines open, take the drum and head inside the tree. Click the hand on the seat-like structure at the center of the screen. Pick up the branch which Forest Heart gives you. Talk to her to ask her about the "Wise One". Leave the way you came in. Enter the next higher entrance which you can see on the side of the tree, gather some of the seed pods, ecord them, and leave. There is a third entrance a little higher up (or around) the trunk, which is less visible. Enter it. Pick up the bark cup and collect some of the sap from the pool, then leave. Return to the village.
The Grove People
Ecord the pot that the woman with the baby is making, the squatting man, and his iguana. Talk to the woman, the baby, and the squatting man (the chief). Go east. Ecord the pot with the fire under it and the hunters at bottom right. Talk to each of the three women standing around the pot, the weaver woman, and the woman sitting by the garden plot. Continue east. Ecord the bright berries growing across the river, the man thatching the hut, and the bench outside the hut. Talk to the boy, then give him the drum. Talk to the man twice, then show him the seed pods or cup of sap. Put them both on the stool. Swing across the river on the vine. Pick some of the berries. Get the necklace that you find under them. Return to the village screen, then come back. Get the poultice from the bench and go give it to the woman with the baby. Show her the necklace. Give the necklace to the weaver. Talk to the chief. Take his machete. Give it to Sumac. Give the roots to the rightmost of the three women at the pot, then give her your cup. Go west. When the butterfly lights on the flowers, ecord it, then use the cup of sweet drink on it. Pick up the cup when the butterfly lands on it. Give it to the man outside the shaman's hut, then follow him inside. Ecord the rattle over the door, the mask, the charm (thing near the mask on the right), the bowl of water, and the shaman. Click the hand on the floor to sit. Click the leaf on the ceiling where the leak is coming from, then sit down again. Put the berries in the bowl. Click on the symbol that is named as the shaman indicates, then click it on your face in the bowl. Give the shaman the branch from Forest Heart. After the vision, pick up the golden blossom that fell at the bottom of the screen. Talk to the bat. Show her the amulet. Click the hand on the net to untangle her.
The Cibola Campsite
After you're captured and tied up, click the walk icon near the cage to bounce the chair over there. Eat the carrot that's holding the cage shut and Paquita will free you by chewing through the ropes. Exit the room. Take the fax from the machine next to the television. Open the zebra footlocker and take the tennis racquet. Take both sheets off the bed, and get the organizer that's under them. Examine the tail of the jaguar rug, then click the hand on it. Get the piece of paper and read it. Click the inventory hand on the organizer, turn it on, and press the button with a key on it. Enter the password (RETHGUALS). Make a note of the numbers (582) - they're the combination to the safe. Open the safe and get everything inside it. Look inside the wallet. Ecord any of the animal items in this room. Move the rug and click on the chink in the floorboards. Combine the sheets to make a rope and use the rope on the hole in the floor. Climb down the rope.
Wait for Gonzalez to start reading his cookbook. ("Did Forrester's dance make anyone else physically ill?") Ecord the "garden" plot, the river, and the ground of the campsite. Click the hand on the oil drums in succession to hide behind them. When you get to the bottom-most, wait for Gonzalez to leave the screen. Quickly climb the tower and turn off the alarm (the box attached to the dish). Get the hand vacuum and search the laundry basket to find a pair of suspenders. Tie these to the alarm box, and you will "bungee" back down to the ground. Hide behind the bottom oil drum and get some of the spilled birdseed with the hand vac. Click the hand on the vac in inventory to take the seed out of it. Go back up the line of oil drums and re-enter the shack. Leave again and Gonzalez will be back reading his cookbook. Exit the screen to the east, taking care to stay behind Gonzalez. Hide behind the crates. Ecord the birds in the cages and the oil drilling operation. Make your way across to the oil drum by the bird cages, and hide there. Give them the birdseed, then use the key you took from the safe to unlock the cages. Take the axe from the tree stump and use it on the log. Go back inside the shack and talk to Paquita, then return to your canoe and shove off (click the hand on the boat twice). Don't worry about the things you lose, you don't need them. Use the tennis racquet as a paddle. When Slaughter is chasing you, repeatedly click on the far edge of the screen to paddle away from him.
Ecord each of the varieties of bat (except the ones hanging at top left - you can't get those), and talk to them. Show the amulet to the bat sitting at the desk. Pick up the stack of visas and distribute them to the right bats. Check your ecorder to find out the scientific name of each of the bats. Talk to each one again before giving it the visa. Show the leftover leaf to the official bat, and exit the cave behind him. Ecord the bat, the stone with the symbol that looks like two crossed swords, the reliefs near the bat, and the carving at the bottom of the screen. Click the hand on the pole sticking out from the wall near the hanging bat. Talk to him. Click the walk icon on the ground to get down. Pick up the glowing stone at the left of the screen. Place it in the niche at the very tip of the base of the jaguar statue. Answer the riddles (they're fairly obvious). Take the golden feather. Exit the screen through the cave at the top. As you proceed down the path, Paquita will enter and then fall down sick. Exit back the way you came; you will automatically talk to Chiropterus and bring him to Paquita. After he gives you the whistle, blow it to clear the bats from the exit, then get in the boat.
The Flooded Forest
After your boat is sunk, ecord the water and the round fruit on the trees. Swim south. Ecord the lily pad. Climb up the vine and pick a banana. Swim north, then east. Ecord the white thing on the island with the howler monkey. Talk to him and give him the banana. Climb onto the rock and take the piranha jawbone. Jump back in the water and return to the lily pads. Cut one free with the jawbone. Hop onto the lily pad and head back to the monkey. Get off the pad. Oh great - now you're eagle fodder! Ecord the eagle. Give the golden feather to the Empress Eagle.
The City of Gold
At the overlook, ecord the two bunches of pink flowers at the bottom of the screen, the city, and the jutting rock. Clean up the litter. Take the magnifying glass that you find under one of the pieces of litter. Use it to examine the necklace you got from the weaver. Examine the two gold face masks. Click the hand on the one you have in inventory, then place it in the empty space. Pick up the pile of gold, and put this on the seat along with the gold disc you found in the mask. Go down the stairs. The path through the city is basically a loop that doubles back on itself. The pattern on the necklace was a map, but it's hard to see. Ecord the city again and one of the short, upright sections of stone. Head to the right and just follow the path (there's only one way you can go). Inside the high room, ecord the stone above the mosaic. Click the tiles until you get a matching border of double yellow stripes all around. Ecord the pipes, then take them. Click all the tiles once to get the matching zigzag border. Take the cup and crown. Climb up the wall next to the niche. Click the hand on the carving of a serpent. Exit the room through the revealed doorway.
Click the hand on the islands to jump to them. Skip the leftmost of the small islands, unless you want to be dunked by a turtle. Click on the water once you are on the island with the seat. Wear the crown and play the pipes. After the snake falls asleep, swim to the far island. Ecord the fountain and take the stone cup from the smaller statue. Put the stone cup in the niche near the vines, and put the golden blossom in the cup. Click the hand on the head at the top of the fountain. Show the amulet to the flowers. Talk to them each twice. Turn the head on the fountain again. Take the seedling. Watch the scene.
While Slaughter is digging, jump down from the stela. Place the cup of gold dust on the fountain. Use the whistle. Get some water to give to Paquita. Watch the scene. Plant the seedling in the circular space. After you see it grow, before calling Paquita again, turn on the Ecorder and select "Test Myself". For each picture shown you have to identify which of the two ecorded items it is. When finished with the test, blow the whistle. Look under Paquita's wing.