Well here I'm going to post my ideas for custom instances.
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Jurassic Park
Lore: This area used to be a peaceful place until a strange portal opened up. Hordes of monsters that resembled dinosaurs started appearing in the area, they were huge, aggressive, and only seemed to help there own kind.
Type of monsters: Of course your going to need some dinosaurs for this area, my idea is to use the dinosaurs from ungoro crater, or maybe find a different skin for them from model viewer.
Area: The best places that I can think of are Zul'farrak and Zul'Gurub, I'd reccomend Zul'farrak since it's a lot smaller and easier to find your way around.
Other details: For my server for the boss's I put a remark to every GM on the server for instance Jordactyl.
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The Graveyard of Elves:
Lore: Ever since kil'jaeden started being summoned, there has been a disturbance with the magical balance in azeroth, this has caused many of the ancient dead elves to be revived. Now they roam lose as undead causing destruction.
Type of monsters: For this one you will want quite a bit of spirits and throw in some of those crack elves near the blood elf starting area, and maybe put kael'thas as a crack elf as a final boss ( or not if his displayID is only in PTR ).
Area: The best place I can think of is SM graveyard but if you think it is too small for your tastes you could also try stratholme.
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King Leviathan's Lair:
Lore: King Leviathan has been in deep sleep for hundred's of years, now he has been awakened by the sudden mining of the land above him by adventure corp. He is not the only one that has been awakened many ancient sealife have also been disturbed. Now they rising once again and causing havoc among the land.
Type of monsters: My best guess for this is for king leviathan is too put a leviathan display, and raise the scale a bit. You'll also want to put a lot of turtles, sharks , and fish.
Area: The only two places for this too be is black fathom deeps and the temple of atal'hakkar, I'd strongly suggest using blackfathom though because it suits the lore alot more, and theres alot of water so you can put sea monsters there.
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Well that's all I can think of, If you got an idea post it in this thread and i'll add all the lore,types of monsters, and the area it should be in.