It's my understanding that many of the vbulletin.org modifications are custom changes that haven't been released as mods (why? I don't know, but I think making the modifications is one thing, packaging them as mods and supporting them is another - maybe it's just that there's no one to do that work).
As for moving the thread controls to the top, it seems like it would just be a matter of editing the appropriate template to move the code. I think that mod you linked to is just a text file with instructions for editing the template, so maybe you can use it to figure out how to do the same in vb4.
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