Alright, I'm going to try to break this down in pieces
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.
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.
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.
Okapi and bird mixes have been fine before. Though I do suggest giving the Shoebills plenty of space to get away from the Okapis.
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.
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).
I wouldn't mix Pheasants with Macaques, I suggest keeping the Pheasants separate as, even with deer, there might be risk of trampling.
Kiwi have been safely kept with Boobook and Barn owl, this should be fine.
Both of these should be fine.
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.
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.
I would advice against mixing snake species, even though snakes have been mixed before, it's better to not take the risk.
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.
Thanks for this extensive list & help you've provided.
I was also wondering about:
1. Dugong & Sand Tiger Shark?