If it's just about the navbar, I suggest only making the navbar be in an iframe, not the content. This way, you only need to edit the navigation file, and the change appears everywhere on the site.
An issue here seems to be that if you wanted to display the content pages in an iframe, you'd have to make them so they don't have all those things at the side there, like the lace and the chocobo images etc. If you look at the image in my attachment, notice how it has the sides of the page twice? Not only around the content area as it should, but also inside the content box, before having another content box finally with the content. If you make your content in an iframe, only the index page has those sides defined, the content pages only have the content text, basically. I hope I explained that in a way that makes sense.
The reason why I'm explaining this although you might know it already (since you have parts of the site which display this correctly), is that the gifs only stop moving when I enter a page that displays the sides twice, and then click out of it. Other than that, the gifs move fine for me.