Part of your performance issues may be the way you're selecting elements in your jQuery.
Take this selector:
Code:
$("#nav-wrap #navigation #navigation-wrap #top-logo")
In CSS, this would be slow, then consider that jQuery has to run everything through some JS to perform the same function that CSS does natively.
Why is it slow? Here's what's happening:
Browser: "Looking for #top-logo - Ok, found it!"
Your Code: "Screw you, keep looking."
Browser: "Looking for #top-logo within #navigation-wrap - Ok, found it...again."
Your Code: "Screw you, keep looking."
Browser: "Looking for #top-logo within #navigation-wrap, within #navigation - Ok, found it...again."
Your Code: "Screw you, keep looking."
Browser: "Looking for #top-logo within #navigation-wrap, within #navigation, within #nav-wrap - Ok, found it...again."