You can't change the coordinates of the box to rotate according to your mesh - you'd have to expand the box so that it became a new bounding box. It's not difficult, but it's unlikely to be accurate nor fast...

Instead, I would give some thought to changing the ray position and direction. I've not double-checked it, but if you multiply the ray position by the world transform they should be in the same coordinate spaces again - thus checking on the original box (with modified ray) will be correct.

hth
Jack