See the Codex section on jQuery noConflict wrappers in WordPress:
[…]if you really like the short $ instead of jQuery, you can use the following wrapper around your code:
jQuery(document).ready(function($) { // Inside of this function, $() will work as an alias for jQuery() // and other libraries also using $ will not be accessible under this shortcut });
So, in your case, you could use
var seq = 0;
jQuery(document).ready(function($) {
$("html").niceScroll({styler:"fb",cursorcolor:"#000"});
$("#mainlogo img").eq(1).hide();
function goSeq() {
var nxt = (seq+1)%2;
$("#mainlogo img").eq(seq).fadeIn(2000);
$("#mainlogo img").eq(nxt).fadeOut(2000);
seq = nxt;
setTimeout(goSeq,2500);
};
goSeq();
$(window).load(function(){
setTimeout(function(){
$("#gmbox div").animate({'top':60},1500,"easeOutElastic");
},1500);
});
function trackLink(link, category, action) {
try {
_gaq.push(['_trackEvent', 'tracklink' ,'click',link.href ]);
setTimeout('document.location = "' + link.href + '"', 100)
}catch(err){}
}
$('[rel="outbound"]').click(function(e){
try {
_gaq.push(['_trackEvent','outbound','click',this.href]);
}catch(err){}
});
});
…assuming that all the rest of your JS code is correct, of course.