Compatibility view tries to emulate ie7 standards mode which it does but not perfectly. Your layout is therefore most broken in IE7 also. If you are triggering compatibility mode yourself then I wouldn't bother with it but if its being tripped automatically then it may be recovering from a fatal script error.
The overlap on the footer is easier and you need to pad out the bottom element because of the sticky footer. Other browsers are automatically placing the footer below but IE7 needs to be padded out by the height of the footer.
I couldn't get a local copy working properly with all those scripts but in the basic version I got working there was no overlap of the right column in IE7 so it does seem to be the script issue or the CSS files that your are swapping.