How did I know it was caused by WordPress SEO plugin: it was the last plugin I had installed. So I enabled/disabled it a few times and saw that the problem appeared when this plugin was enabled (although it was not caused by the plugin per se)
how did I find out magic member was causing the jquery version clash: I got lucky. I went through the admin screens of m theme and all installed plugins till I found a configuration for the jquery version in the MagicMember admin screen. I changed it to use the latest jquery version and the problem went away.
If I had not found a configuration in any plugin screen then my next move would have been to do a grep through the code of all the plugins and theme to see if any jquery tag was hardcoded somewhere. You can also use chrome's developer tools to see which JS resources are being loaded and see if that provides any clues.
Hope that helps.