Take upallnights advice and find out what size hubcentric rings you need to put E39 rims on an E53. BMW wheels are hubcentric which means they center based on a tight fit between the hole in the center of the rim and the protrusion on the hub. If you don't have a tight fit (hubcentric rings act as "shims" to provide a tight fit), the wheels won't be perfectly centered on the hub and will vibrate/wobble as you are describing. If your rear rings are good, move them to the front as the fronts are more sensitive to eccentricity than the rears.
The other classic cause of freeway vibration is worn front thrust/control arm bushings. These are the two things I would try first.
2008 Lexus IS250
2001 BMW 530i
1999 Lexus RX300