The COOP plugin puts the archive code above everything. Is there a way to modify that so it shows up in the footer of the archive?
Correct. I have changed the plugin that it uses from archive_process_start to archive_complete and the links still show but now they show at the bottom and will be more compliant than being located in the <head> tag. You can see it here: http://www.mustangevolution.com/forum/archive/ Any reason they were put there?