I have not modified the javascript files one bit, nor have i missed out on any elements that were originally in the vBulletin templates.
They were of course, linked to <table>, <td> and the like, which doesnt fit with schemantic markup for most things (popup menus should be unordered lists imo), so mostly they're assigned to other element types.
So far, I think I may have found the solution. I worked out that I did infact miss an id="edit$post[postbit]" at the start of the postbit, which has fixed the quickedit somewhat.
As for the popups, I think it has something to do with me removing style="display: none;" and replacing it with a class. Will let you know
And the XHTML transition is a PITA unless you know your way around css and xhtml completely imo. It really is a shame there isnt a default style with more "proper" markup.
And thats what it was! Luckily I decided to dedicate time to understanding the javascript which now I do