Heya! Some secrets and goodies in this hack are hidden fairly well, and I can understand that searching for such things isn't fun for everyone. As such, I've included a list of locations for all moons (in case you're interested in the Lunar 100% speedrun), and all secret exits. Portrait Rooms are not included in this document, though- they only exist as nice secrets in the game, so there's no reason to help you find 'em ;) Enjoy! If you don't want spoilers, scroll at your own risk.
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SECRET EXITS/AREAS:
Catnip Canyon - The key is in the upper half, above the moon, and the keyhole is in the lower half. To access the keyhole, stand on one of the layer 2 platforms that would usually sink into the lava. You'll know the one by the hole in the roof above it.
Wishy-Washy River - If you make it to the moon, running right will grant you a P-switch! Use that at the 4 blue pipes to reveal a pair of blue doors, which lead to a kaizo speed-route through the level!
Netherworld - At the first section, take the P-switch and activate it. A coin trail will take you back to a door on the left, for a secret exit! This will lead to the Yellow Switch Palace.
Dark Astoria - On the second skull raft, you'll want to claim the shell from the koopa you must navigate past. Use a shell jump to get up to the rope platform and claim the moon, and the pipe will lead to the secret exit! Beware though, you'll need to have beaten the full secret exit of Catnip Canyon to proceed.
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MOONS:
Grizzly Hills - Above the first fire lotus, spinjump. Likely to be offscreen, visible by running with p-speed!
Catnip Canyon - Visible on the upper route, also a clue for greater things! Obtain via multiple methods. Easiest method is taking the spring back from the checkpoint!
Catnip Catacombs - At the first section, bounce through the hold above the thwomp, and maneuver past the sideways thwomp above it.
The Old Garrison - At the first section, bounce up the wall above the chuck throwing rocks. You can do this by bouncing on one of the rocks at the peak of the chuck's throw! The platform above holds the moon, hidden from sight.
Wishy-Washy River - Moon is claimable via a series of koopa jumps at the start of the level. Another nice clue for greater things!
Cloudy Meadows - After the muncher tunnel, use turnbacks with the cape (turnback patch is enabled, so spins will be consistent with this) to claim the moon!
Netherworld - At the end of the second room, you may either jump off to claim the moon, or bounce of the disco shell mid-air to claim it without dying! Good luck!
The Tower - In the very first section, there will be a pair of moving platforms. If you're fast enough, you can jump up them onto the ledge above, which holds a moon!
The Trove - This one's easy, just find it at the end of the P-balloon section, in the air!
Dark Astoria - On the second skull raft, you'll want to claim the shell from the koopa you must navigate past. Use a shell jump to get up to the rope platform and claim the moon!
Steel Canyon - At the second pair of chucks, when you're using them to break through walls, there'll be a dark pipe you jump up to by bouncing off of one. Go into that pipe, and complete the challenge to get the moon, as well as a friendly greeting!
Shifting Fortress - This one's a toughie. To claim the moon, shown above the end of the first section (where you P-speed run to the first H) you'll need a cape. To claim said cape, the hard method is to avoid losing your mushroom-state until you reach the ?-block after the on/off switch, above the thwomp. The easy method is to go past it, to the little chamber where two thwomps guard a mushroom (indicated with coins) and only then double back to claim the cape. Do not grab the ?-block if you aren't Big Mario, or else you'll just get a mushroom! From there, fly over and grab the moon. it's suspended in the air at the end of a giant arrow- hard to miss!
Airshipvania - In the cape section, go left instead of right when you fly up. You'll find the moon suspended in the air. 
Polyphonic Palace - In the third section, there will be a yellow switch block containing a mushroom. Carry that mushroom through the full section, and you'll be rewarded with the ability to claim the moon, right before the pipe.
Journey - You'll see the moon - you just need to do a backshot shell jump off the wall to claim it!
Folivora Cliffs - After the first checkpoint, drop down the chasm in front of you, and jump off the wall to land on the pipe, claiming the moon. The pipe will take you back to the checkpoint!
Moisty Mountains - At the end of the level, bounce off the oncoming Pokey to nab the moon.
Between - At the very end of the level, go left! The moon is waiting for you there.
Arisen Peak - At the end of the level, a ?-block contains a key. Use it as a platform and keyjump to get up to the moon at the pipe you entered from.
The Purple Pinnacle - At the start of the second section, bounce off the saw mid-air to nab the moon!
If you manage to beat all levels and claim every moon, congrats! You're ready for the Lunar 100% speedrun ;)
