The first issue is a bug with the VaultWiki mobile style that comes packaged with the product. Since vBulletin 4.1.11, the Mobile Style has been a separate Master Style, so instead of inheriting unmodified templates from the original Master Style, it considers that they don't exist. This results in all wiki pages being invisible while viewed under a Mobile Style post vB 4.1.11.
I have fixed the issue of articles being invisible, but there are likely other issues due to missing templates.
As for the logo being too wide, the only thing I can think of is to create a different logo with no text. I can't imagine a way to shrink the existing text without it becoming unreadable.