I'm thinking the tightened bolts are not tightening enough. Maybe you need to add a flat washer under the lock washer and the nut on the bracket side of the motor mount. I would do the extra washer on both sides of both rubber mount/brackets. Maybe someone cut the slot in the bracket too long.

its also possible the headers are at the wrong end of the allowable tolerance and the tube is too close. Can you hammer clearance the header tubes for extra clearance?

With your description that it was correct and the motor sat level, then a week later the motor was no longer level and the header was rubbing, I would go with the extra flat washers 1st.