Ok I wish I had made a step by step list I did not..but Here are some of the critical things lets try there first...
Plugin Config fo QM heres the whole thing if you just want to add..
&1=undefined;; &jqpath=Path to jQuery;text;assets/js/jquery-1.9.1.js &loadmanagerjq=Load jQuery in manager;list;true,false;false &loadfrontendjq=Load jQuery in front-end;list;true,false;false &noconflictjq=jQuery noConflict mode in front-end;list;true,false;false &loadtb=Load modal box in front-end;list;true,false;true &tbwidth=Modal box window width;text;80% &tbheight=Modal box window height;text;90% &hidefields=Hide document fields from front-end editors;text;parent &hidetabs=Hide document tabs from front-end editors;text; &hidesections=Hide document sections from front-end editors;text; &addbutton=Show add document here button;list;true,false;true &tpltype=New document template type;list;parent,id,selected;parent &tplid=New document template id;int;3 &custombutton=Custom buttons;textarea; &managerbutton=Show go to manager button;list;true,false;true &logout=Logout to;list;manager,front-end;manager &disabled=Plugin disabled on documents;text; &autohide=Autohide toolbar;list;true,false;false &editbuttons=Inline edit buttons;list;true,false;false &editbclass=Edit button CSS class;text;qm-edit &newbuttons=Inline new resource buttons;list;true,false;false &newbclass=New resource button CSS class;text;qm-new &tvbuttons=Inline template variable buttons;list;true,false;false &tvbclass=Template variable button CSS class;text;qm-tv
But Among other things You will notice that I updated the path to query-1.9.1.js (the min JQ I just took out .min part , I was previously using I think 1.45, I read that MM relies on 1.9... so that may have played a step I did have to copy that .js to there...
Plugin Execution Order: (relevant ones where both MM and Qm are called, I think...I added the "onBeforeDocFormSave: as a 'system event' to QM one of those... )
And Finally My Template was already calling Jquery, Since I wasn't sure which version ..I just made sure it was the same as what MM and QM rely on. So in this case - again I may have even copied over..
I hope this helps at least a bit.
Ill check back at a later time to see if there is anything else I could share..