Ok first of all, put your code in the bottom of the layout.master page, if you see the code of the page the scriptmanager is inside the form so if you put the script in the header the scriptmanager don't find the code. Secondly Jquery is already port of mojoportal so you don't need to add a reference to it. If you want to add the jcarousellite put this in the ClientScript folder under your data/sites/1/ClientScript/
I don't now if you new about it but, there is a slideshow function in the html module, give a try, and may be you can achieve what you look with out adding the script.