This game operates on LucasArts rules, so you can't get killed and it isn't possible to put the game in an unsolveable state (I hope). I've tried to anticipate trouble spots, but if you get stuck somewhere else, please feel free to contact me. Good luck!
How do I...
...get back out of the Blue Shrine?
...wangle this key out of the aquarium?
...get back to the top of the cliff?
...get over the wall to the north?
...conquer my fear and enter the cavemouth?
...escape from the Red Shrine?
...squeeze into the cathedral?
Go up from the first room and you'll find an idol embedded in the trunk. TOUCH it and gain the power to MIMIC animals. You'll need to use it on the flying squirrels, but they're too far away. Try to TAKE the overripe golanut and it will fall into the plane, followed by the squirrels. Now you can go back down and MIMIC them. Now you can go down from the plane to the forest floor!
You'll need to use MIMIC again, this time on something that can swim. Try the pirahna in the aquarium in the Fancy Quarters on the pirate ship.
You'll need the master the DRINK and DRENCH abilities to escape from here. First, make sure you have them by OPENing the clam and TOUCHing the idol. Then DRINK WATER to fill your water reserves and DRENCH the dried mushroom. The water will swell it, allowing you to exit to the southwest.
You can't lift the aquarium, nor can you break it, and you can't reach in because of the pirahna. The solution is to lower the water level by drinking it, but before you can do that you need a couple of things. The first is the DRINK/DRENCH ability, which you'll get from the Blue Shrine past the waterfall, so you can physically drink so much water. The second is something to keep the pirahna from chewing your lips off. Take the bamboo tube from the Jolly Tavern and USE it on the aquarium. The water should lower and allow you to take the key!
Alternately, if you have the HEAT ability and aren't too virtuous, you can HEAT PIRAHNA and just fry the sucker.
If you're stuck at the Great Stone Gate, you need to head back south and explore the pirate ship and surroundings. Once you've done everything there, you should have the ability to get over the wall. (See 'Getting back up the cliff', above, for further details.)
Only someone truly courageous could muster the guts to enter. Fortunately, courage comes in liquid form nowadways. Retrieve the golaberry wine from the Jolly Tavern and DRINK it. You'll need a couple of drinks in you to enter (three is too many), and they do eventually wear off.
He's keeping a close eye on that passage. You'll need to blind him, just for a moment. Notice the steam in the room. What if you dropped a lot of water on that pit of lava? DRINK WATER at a source and DRENCH the lava. The ape will be blinded long enough to sneak past, but not for long, so hurry! After the first time you get past him, he gives up entirely on stopping you due to severe perfectionism.
Just like with the other shrines, you need the power you got from TOUCHing the idol to escape. Notice how the lava is thick and congealing. It's hot, but it could be hotter. Try HEATing it and you can catch a ride back to the surface.
How can you fit into the cathedral, retrieve all those goodies, and enter that tempting trapdoor?
You can't. Ever.
Fortunately, what you actually need is to get into the tunnel under the cathedral. Passing through the trapdoor is irrelevant. If you were strong enough to pick up the whole church, you could just move it aside. But how to get that strong? Pay a visit to the Sauna of Kong (see "Entering the cavernous cavemouth", above, if you're stuck on that) and MIMIC the ape. Now you've got the strength of mighty Kong himself! Trying using TAKE on the cathedral. You can't actually carry it around with you, but you'll pick it up and move it to the side, allowing you to go DOWN the tunnel. As for all that gear in the cathedral, unfortunately, you cannot get it.
Except for the useless doorknob. That's all yours!
This one's a doozy but bear with me. To playing the organ effectively requires several steps.
First, you need something to play. The sheet music from the Jolly Tavern will do nicely, so bring it along.
Next, the organ needs to be operational. If you look at it, you'll find an empty steam tank. DRINK WATER from a source and DRENCH the tank to fill it, then HEAT the tank to get it producing steam.
Finally, you'll need to give each of the three statues a particular instrument:
St. Brachiatus needs the old drum. You can find in the shelter at the Overgrown Campsite--the shelter is so old that just looking at it will destroy it, and the drum is inside.
St. Prehensilus needs the coconut bell. It fell off of the cathedral when you lifted it.
St. Bobo needs the gold fiddle, which is locked behind a portrait in the Fancy Quarters. Retrieve the key from the aquarium (see the section on retrieving the key if you're having trouble) and USE it on the portrait to reveal the booty.
Once you do all of this, you can play the organ. Have fun!
Vola wants an offering and if you give her the wrong one, she'll eat you instead. In fact, this is just want you want her to do, so just give her something. Once you're in her stomach, LOOK at the fedora-clad skeleton to loot him and find a number of object, including the final idol. TOUCH it to gain the warp power, then WARP TO the sketch you found on the skeleton in order to escape. Congratulations, Jungle Queen!
There are two ways to finish the game. There's the direct route: once you've got the warp power, go to the Volcanic Path, where you can see the city, and WARP TO CITY. You can also pick up the component from directly under the plane, WARP TO PLANE, and USE the component on the radio to fix it so that you can USE the radio to call for help. You'll get different results depending on which you choose.