Hi,
I just updated that document
http://www.mojoportal.com/adding-custom-javascript.aspx
in the latest version of mojoPortal you don't have to use a UserControl nor pre-render events to add scripts that depend on jquery or jqueryui because we load the jquery and jqueryui scripts in the head so your scripts will always come in after them.
As far as IE issues/errors with your own custom scripts, you'll have to figure that out yourself.
Best,
Joe