I seem to have worked around the issue by first, making sure the sideboxes didn't load during checkout, then creating override folders (one for each of the checkout pages) in the template directory with a customized html_header.php that only loads my analytics jscript file, the rest I deleted the calls from the html_header. I tested checkout and it works fine, but will this create any other problems for me? I'm completely php illiterate almost.