Note that these changes are assuming starting from a base where the required mods are installed:
Zion Trail (and patch 1-11)
Zion Trail Enhanced
Zion Trail Tweaks

Not a hard requirement, but it’s been removed from nexusmods. Will update sometime soon to tweak some things to account for playing without this:
S6S Zion Trail Patch

Mojave-Trail-Zion linkages:

• The Honest Hearts DLC now properly starts if you enter Zion Canyon via the trail. If you do this, the Happy Trails Caravan will be removed and dialogue options implying that you had traveled to Zion Canyon via the caravan will be removed or tweaked. Follows-Chalk will meet you at the welcome center just down the road Zion Trail puts you on.
• Mojave Northern Passage now links to a new cave entrance in Zion Trail I added, about 1/6th of the way through the trail. You can enter Zion Trail this way if you have the map.
• A new proper Southern Passage interior has been added, which links the Sothern Passage location in Zion Canyon to north-west of Zion Trail. You can enter Zion Canyon through this passage. Doing so will remove the Happy Trails Caravan and apply the same dialogue changes entering throug the road does.
• If you have the trail map, you can leave Zion Canyon at any time through either location. Any tribals following you will be fired, and you’ll fail Follows-Chalk’s Bighorner quest. Note that during the final sequences, you’ll be prevented from leaving.
• Upon finishing Honest Hearts and leaving the valley into Zion Trail, you’ll be presented a message and all zion trail exits to Mojave and Zion will be fully revealed on your pip boy, allowing you to fast travel back to the Mojave right away if you can’t already.
• Going backwards into the Route 95 checkpoint will now unlock and open the gate if it isn’t already
• The Happy Trails caravan can now die pre-dlc. If they die, your only way to get to Zion Canyon is through the trail quest.
  These changes make the Zion Trail more properly integrated in the game, allowing any order of play, and allows skipping the trail via the caravan.

Items:

• Fixes from Tale of Two Wastelands have been brought forward (but should probably still be ok in fallout nv)
• Food items added by Zion Trail now get improved by the fallout 3 food sanitizer. This is for Tale of Two Wastelands, but should work with other mods which restore the item.
• Items have been added to form lists and merged with complete fix records
• Brought forward S6S’s book name changes to other records which mention the book names.
• Fixed crashes that could happen when using a Zion Trail skill book.
• Changed skill book corner message to instead be a message box.
• Changed skill book gag messages to fit S6S’s new book names better.
• Fixed Vault 66 suit icon still saying 616.
• Tweaked names of items to make them fit better in the game.
• “VaultTec” > “Vault-Tec”
• “Scarf - Red” > “Red Scarf”
• “Carry Sack - Large” > “Back Carry Sack”
• And other similar changes

Level changes:

• Zion Trail’s Laboratory Sets now act like Mojave Chemistry Sets.
• Neville’s control panel can no longer be activated, since it does nothing.
• Magazine Vending Machines can now give magazines, like those in the Mojave.
• Changed some key-only locks to instead be leveled. Affects mostly those doors in Vault 66.
• Moved the box in the Sheriff’s Office closer to the jail cell (and locked it) so the quest doesn’t get softlocked by the dude sitting too far away to talk to. The box gets unlocked when done talking to him.
• Added a tiny secret if you climb somewhere near the Mojave car tunnel. :)
• Added Zion Trail map markers: Zion Overlook Tunnel
• Renamed Zion Trail map markers: Zion National Park > Road to Zion Canyon, NCR Checkpoint > Route 95 Checkpoint
• Added Lillypad Field map markers: Cave to Zion Trail, Cave Path, Hunting Shack, Island, Pondlurk Nest
• Added Zion Canyon map markers: Road to Zion Trail
• Fixed positions of the pip-boy maps in new worldspaces so locations line up properly with roads. Also adjusted the colors of the maps so they are consistent with base game.
• Attempted to fix Lillypad Field pondlurks not spawning.
• Worked around an issue that would arise if LOD is generated for Zion Trail. The trees would turn into big white squares. I’ve placed blank images where textures were missing, so instead of white boxes being in the distance, trees will just pop in, which is much more favorable.
• Fixed a lot of object placements:
• Replaced static coffee mugs with misc item versions.
• Replaced static milk bottles with misc item versions.
• Replaced static drinking glasses with misc item versions.
• Replaced static metal cooking pots with misc item versions.
• Replaced static fission batteries with misc item versions. (if they didnt look like they were powering anything)
• Replaced static Rocket Souvenirs with misc item versions.
• Replaced static Glass Pitchers with misc item versions.
• Replaced static Pots with misc item versions.
• Replaced static Brahmin Skulls with misc item versions.
• Replaced baby-mode toy cars with misc item versions.
• Replaced baby-mode baby rattles with static versions.
• Replaced baby-mode toy blocks with static versions.
• Replaced misc item NCR money with the currency versions.
• Replaced misc item Legion money with the currency versions.
• Replaced “new medical brace” items with the main medical brace items.
• Replaced a briefcase model with a lootable version.
• Replaced a garbage can model with a lootable version.
• Replaced static Banana Yuccas with pickable versions.
• Replaced static Coyote Tobacco with pickable versions.
• Replaced static Barrel Cactus with pickable versions.
• Replaced static Honey Mesquite with pickable versions.
• Replaced static Prickly Pear Cactus with pickable versions.
• Replaced a “wind brahmin” with a Tumbleweed.
• Replaced all Lakelurk and Mirelurk egg clutches with new Riverlurk or Pondlurk egg clutches where fitting.
• Replaced all Lakelurks in Zion Trail with Riverlurk Kings. (there were only like 1 or 2 of these)
• Replaces some props which made up a campfire with an actual usable campfire. Only found one of these.

Mechanics:

• Added a challenge for reading all Zion Trail skill books.
• Reverted S6S’s changes to Stoicism. It just seemed quite underwhelming to change a +1 endurance to a +3 survival. Load their esp after mine if you still want the +3 survival.
• Added proper quest markers to Weird Times, Profits of Doom, A Quick Death in Utah, Ghoul Wrangler, Book of Bad Decisions, When We Remembered Zion, We Hanged Our Harps.
• Fixed interactions with mods that delay the Honest Hearts starting quest, which would make White Legs passive, because Zion Trail places them in a few places before you could ever start the DLC.
• You can now interact with the door to Zion Trail before finding the note. It prevents you from entering, but starts the quest with a new stage that points you to the note. Should help people get lost less.

Creatures and NPCs:

• Fixes from Tale of Two Wastelands have been brought forward (but should probably still be ok in fallout nv)
• Added Riverlurk and Pondlurk Meat and Eggs. Riverlurks and Pondlurks now drop these items instead of Lakelurk and Mirelurk items.
• Brought forward TTW fixes for mirelurks and lakelurks to riverlurks and pondlurks.
• Lillypad Field spore plants now spawn loot on death.
• Fixed the inside of some NPC’s mouths being pink.

Compatible with Tale of Two Wastelands via a patch:

• Added recipes for Steamed Riverlurk and Steamed Pondlurk. These only become visible once you’re able to enter Zion Trail.
• Brought forward Tale of Two Wastelands changes to security armors.
• Brought forward Tale of Two Wastelands DR and DT reworks, and item value reworks.
• Brought forward more Tale of Two Wastelands fixes to mirelurk variants.
• Brought forward all Tale of Two Wastelands included quests in dialog topics.
• Brought forward all Tale of Two Wastelands included objects in form lists the main mod edits.
• Added Tale of Two Wasteland’s rebreather breathing to Zion Trail’s rebreather.
• Added Riverlurks and Pondlurks to TTW mirelurk challenge list.
• Added Vault 66 gear to TTW’s vault apparel list.
• Made all Glowing Fungus pickable.
• Made all Brain Fungus pickable.
• Made all BBQ Grills usable as campfires.