The problem is that when called through CGI::Ajax, 'BUILD_CHART' doesn't utilize runmodes. It dynamically builds the XMLHTTP request and, as far as i can tell, is able to bypass the instance script altogether.
Just getting it working isn't a problem -- I can build up and tear down the connections within 'BUILD_CHART' itself with no problems.
It occurred to me while talking this over with a coworker that it's likely going to require a port from cgi to mod_perl to achieve the persistent connection in the background -- that is, unless someone has a better suggestion?