Got your e-mail and forwarded you a screenshot of what those to changes (in boldface) did. It looks right to me, but maybe we are talking about different things. (??)
As far as ‘the mess’, it’s not really out of the ordinary. The theme and the plugin frequently need to have the CSS tweaked a bit to get things to line up. I’m a bit at a loss probably because I’ve been immersed in version 4.0 for months, so the 3.1.2 stuff has become somewhat of a fond memory to me. The JS exceptions would concern me a bit though.
Let me know.
-Mark