Adding my own design in header.
Fragment of a discussion from Project:Support desk
You can set the default skin to Monobook (see $wgDefaultSkin) which was the default on 1.15, and then use your old mods. Or if you want vector (The 1.17 skin), a css rule like:
body #right-navigation { margin-top: 8.5em } body #left-navigation { top: 8.5em }
Would probably fix things.