Alright, I'm going to try to break this down in pieces
1. Marine Iguana, Inca Tern & Great Cormorant
Could be fine, but I fear for the water toxicity levels with two sea birds. Cormorants are also quite voracious and I wouldn't put it past them to at least try to swallow the Iguanas.
4. Crab-Eating Macaque, Proboscis Monkey, Great Hornbill & Plum-Headed Parakeet
In a large enough aviary this
might work, but there would have to be a lot of areas where the birds can come and the primates can't. I would either take out the Proboscis monkey so you're left with the mostly ground dwelling Macaque (and be able to keep them mostly on the ground while the birds can go in the trees), or take out the Macaque and be left with the vegetarian Proboscis monkeys. If you mix them both then the P-monkeys will need climbing structures that the Macaques can use to get to the birds.
7. Mandrill & Black-and-White Colobus-Monkey
Mandrill mixes with other monkeys are rare, but not unheard of. It should probably be fine, but Drills instead of Mandrills would be the safer option.
8. Okapi & Shoebill Stork
Okapi and bird mixes have been fine before. Though I do suggest giving the Shoebills plenty of space to get away from the Okapis.
9. Northern White-Cheeked Gibbon, Sumatran Orangutan & False Gharial
Definitely a bad idea, False gharials are a common predator for mid-sized monkeys. And the Orangutans are smart enough to stay away from crocodiles and might even attempt to kill it. Gibbon and Gharial would be a safer option, but still not really recommended. Indian gharials have very thin snouts that are unable to catch anything other than fish, so they can be mixed with others, but False gharials don't have that problem.
10. Babirusa & Celebes Crested-Macaque
11. Dusky Leaf-Monkey & Visayan Spotted-Deer
Both of these should be fine, though I would switch the Monkeys, as Pigs can be a little more aggressive so it would be safer to have them with a fully arboreal species. Deer and ground-dwelling Monkeys have been proven safe before. (Keep in mind, to have Dusky leaf monkey you need fresh jungle leaves, only a zoo with a greenhouse can hold these animals).
12. Himalayan Monal, Japanese Macaque & Indian Hog-Deer
I wouldn't mix Pheasants with Macaques, I suggest keeping the Pheasants separate as, even with deer, there might be risk of trampling.
13. North Island Brown-Kiwi & Little Owl
Kiwi have been safely kept with Boobook and Barn owl, this should be fine.
14. Przewalski's Horse, Dromedary Camel & Domestic Yak
15. Greater Flamingo, Mute Swan & Canada Goose
Both of these should be fine.
1. Northern Palm-Squirrel, Goodfellow's Tree-Kangaroo, Cotton-Top Tamarin, Kirk's Dik-Dik, Pigeons (Victoria Crowned-, Nicobar), Toco Toucan, Bali Mynah, Raggiana Bird-of-Paradise, Greater Roadrunner, Grey-Winged Trumpeter, Scarlet Ibis, Roseate Spoonbill, Red-Footed Tortoise, Red-Crowned Parakeet, Mandarin Duck, New Zealand Scaup, Paradise Shelduck, Great Argus, Sun Conure, Grey-Headed Flying-Fox, Green Iguana, Hoffmann's Two-Toed Sloth, Common Tree-Shrew & Lesser Mouse-Deer
Unless these are all free-roamers in a very large greenhouse, I would certainly separate some species. Toco toucans should definitely be taken out of the equation, as they'll eat any and all eggs or chicks. The same goes for the Greater roadrunners.
Some other problematic species are the Tree kangaroos, Palm squirrels, Kirk's dikdiks, Two-toed sloth, Common tree shrew and Lesser mouse deer.
If in a greenhouse, half of these should be kept in enclosures, as I feel like they would butt heads.
Tree kangaroos and Two-toed sloths both belong to the same arboreal, slow-moving animal group, so they could get in fights for who gets the branch.
Palm squirrels and Common tree shrew have a similar problem of fighting for the branch, to a lesser extent also with the tamarins.
Again for the Kirk's dikdik and Lesser mouse deer, both miniature ungulates that roam the same area, though in this case I feel like the Dikdik would easily dominate over the Mouse deer.
If I were you, I would make two separate enclosures, one for Tree kangaroo and Mouse deer, and one for Common tree shrew. The rest should be fine free-roaming. Though I would also take out the Sun conures, as they're loud and could cause stress for the Sloths, Iguanas and Tortoises.
2. Cantil & Emerald Tree-Boa
3. Tokay Gecko & Long-Nosed Horned-Frog
Both of these are very bad ideas, and Tree boas and Horned frogs are opportunistic predators and the Mouse deer and Gecko would definitely end up as feeder animals.
4. Asian Vine-Snake & Blue Malaysian Coral-Snake
5. White-Lipped Pit-Viper & Wagler's Pit-Viper
6. Eastern Box-Turtle, Corn Snake & California Kingsnake
I would advice against mixing snake species, even though snakes have been mixed before, it's better to not take the risk.
7. Mozambique Spitting-Cobra & Leopard Tortoise
8. Rainbow Agama & Jackson's Chameleon
9. D'Albertis Python & Beauty Rat-Snake
Agama and Chameleon would be fine. But the Pythons will probably end up eating the rat snake, and the Spitting cobra would be a risk to the tortoise. You could add the tortoise to the lizard mix though.