MMmk… Kalamadea, there are quite a few changes that are going to have to happen. Specifically with the backstory. I'll address any other problems, if there are any, once this is cleared up. 

"Months passed as [Link] wandered in search of his companion, Navi, eventually losing himself in a mysterious forest. It just so happened that this forest led to a parallel world known as Termina." (Hyrule Historia)

The forest in question, for this RP at least, would be the Lost Woods-- Link runs after Skull Kid, falls down a hole, there’s a bunch of weird colorful symbols and faces, and then BAM—he lands on a Deku Flower and is in Termina. You get there by chance—not by choice. And vice-versa. They aren’t in the same dimension. Termina and Hyrule--Neither know of the other.

The history of the Ikana will be the same as the wiki, so there’s also no need to fabricate too much. Let’s at least stick with what we already have-- that Ikana and Termina don’t worship the Golden Goddesses, but instead rely on the Four Giants. And you can’t forget about the Stone Tower, which was obviously meant to be the main source of the Ikana’s curse. It’s a popular theory that the tower may have been built in opposition to the Goddesses or perhaps as something similar to the Tower of Babel. (I'm flexible with that.)

You can elaborate more on the Ikana Kingdom so long as it doesn't contradict anything from the game or wiki or isn't totally nonsensical. I've never been a fan of the theory that Ikana created Majora's Mask in ancient times, but I see the argument and know it's not set in stone-- so I'd be willing to allow it. Not sure how I feel about Majora being worshiped as their GOD though... maybe he once was, but certainly not by the time the moon fell I should think. 

“Though the events which sparked the war between Ikana Kingdom and the nation from which the Garo hail are not divulged, what is made very clear throughout the game is their intense rivalry; it is powerful enough to keep them fighting even after they've died.”

“Details of the countless battles that ensued following the war's initiation are not revealed, but the Kingdom is said to be "stained with a history of darkness" and "drenched in blood," insinuating a merciless, long-winded conflict.[15] When Tatl senses Garo nearby, she says she can sense a "thirst for blood looming all around" them, possible evidence that the war started as, or eventually boiled down to, a conflict of mere bloodlust.” (Zelda Wiki)

Also keep in mind that, in this timeline, Link was never in Termina to save it from the crashing moon. Termina and its well being aren’t really essential to the story, so you have a few options….

Ilgos could have passed into the land of Hyrule whilst trying to escape from the descending moon. Or some other nameless hero/band of heroes could have saved Termina from it’s demise. Either way, Ilgos could not have passed through on purpose. It would have been by accident and he would more likely be alone. I really have no idea how an entire battalion of skeletal Ikana Knights could gracefully infiltrate Hyrule and be apart of the current story. The King would send his Knights to destroy the imposing threat at once-- especially considering what kind of reputation Stalfos have in the Kingdom of Hyrule.