Yeah, compatibility problems are the absolute worse thing ever.

I wish I could be more help, but I'm really stumped why the mainWrapper image is bumping off a pixel.

As for the header, I just realized that I have one of my old 1.3.5 templates installed with the reverse navbar.. the same as yours. So, I compared page sources and ours don't match.

On mine, the code starts out as mainWrapper-logoWrapper-taglineWrapper-headerWrapper-navMainWrapper.

Your's goes mainWrapper-headerWrapper-logoWrapper-taglineWrapper-navMainWrapper.

So, that may account for the header/nav space due to improper nesting in the tpl_header.php.