Silly question - when was the last time the tires were balanced? The e39 was notorious for getting wheel shake from a slightly unbalanced tire. You wouldn't feel it during normal driving but as soon as you got on the brakes, you could feel it. Certainly not trying to discount the fact your rotors may be warped but you may want to insure the easy stuff is out of the way before calling BMWNA.
BMWCCA Member 368765
2008 BMW 535iA | Cobb stg 2+ | FBO | Meth