Running the code quickly through DreamweaverCS5, there are multiple spots where IE6/7 will have problems.
line 154 and 163: Positioned containers define a new stacking order, even when the computed z-index of the container is auto. This can cause positioned children of the container to appear above other positioned elements on the page when they should not.
176 possible: If line-height is defined for a block, it will collapse by half for any line that contains an inline replaced element (img, input, textarea, select, or object).
Numerous:
If a link with display: block and no explicit dimensions is inside a list item, any spaces or linebreaks that follow the list item in the code will cause extra whitespace to appear in the browser.
Affects: Internet Explorer 6.0
Likelihood: Very Likely
line 480:
Any content that does not fit in a fixed-width or -height box causes the box to expand to fit the content rather than letting the content overflow.
Affects: Internet Explorer 6.0
Likelihood: Likely
Not to mention you’re pulling a lot of javascript. I use Jquery fairly extensively and we have to test for IE6. It usually works and only has issues when setting CSS properties or manipulating elements with specific paddings/margins so that framework (which is all javascript) is fine but possibly, if in your other .js files you are using anything to position or move elements, you may have some issues.
Initially though, it looks to be all css-related and things like removing comments where possible as mentioned above.
Could download IETester for free on a Windows machine and see from IE5 through 9. Also, if on a Mac IE5.5 is pretty close to what IE6 on Windows renders. If, by any chance you’re on Citrux, they use IE6 for the browser.