You can insert mobile menu items using a UserMenu extension.
The new Block Manager has a "global footer" area for this purpose.
The Advertisements in v5 are much more flexible than in v4. You can show an ad in specific components (e.g. in Forums but not in Blogs). You can also show an ad after post X or every X posts.
In addition, you can now create a Pages block to show an advertisement, so you can drop that anywhere.
Anything further would use template hooks, as Matt said.
Without knowing how the ad script works, it's hard to say. This seems like something that was designed specifically for your site(?), in which case you could probably adjust it to work with the attributes, as Ehren mentioned. Regardless, I'm 99% certain there is a clean way to handle this, but again... without knowing exactly how the script works, it's hard to say.