I would recommend adding an init or config function in the external js file. That function would be called by script code in pagelayout.tpl that would set the variables you need.
target_url=''
timeout=0
function init_ajax(in_url,timelimit)
{
target_url=in_url
timeout=timelimit
}
function do_ajax()
{
sendRequest(target_url) /* Sample code, may not be correct syntax/call */
}
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