Did you ever find a solution for this? I've been racking my brain for this for a few days now myself. I've found that using wp_head() and wp_footer() around the ajax loaded content will allow it to work, but of course this re-registers/enqueues the scripts (which are already running) which eventually breaks the site after closing and reclicking the modal link. Not to mention that it takes forever to load the modal. Any guidance or workaround you've found would be helpful!