2nd sidebar in the wrong place - please help.

use box-sizing: border-box; for things you add width to that you really should not. This will not help old browsers that do not understand what that is, although you can polyfill for it.

When you add a border it adds width, its that extra width that is breaking the layout. You should notice that the original does not have such borders and was not designed to have such a thing, not without the use of box-sizing or an inner wrapper on the side bar regions.

The menu has all sorts of margins around it on various elements. Use firebug etc to find and remove or override.

Tip - if you ask for CSS help be sure CSS aggregation is OFF, I can tell you that none of us can be bothered debugging your changes against aggregated CSS, because we cannot tell where a particular bit of CSS is coming from.

The version you are using is not 7.x-3.x, if you were there would be inner wrappers on the regions which you could use for the borders on the sidebar regions.

Please do not change the priority, support requests are never critical (critical bugs means the software is crashing your site sort of thing).

If you are cunning you will make region templates for the sidebars and add the inner wrapper in those ;)