What is your milage on the car? If around 180,000km, please be prepared for gearbox to pack it in between then and 200,000km. This is due to the design of the clutch packs in the box. Wears out by that time and there's nothing you can do to stop it from happening.
This is the #1 major overhaul item on the E39. A faulty warnout gearbox will rob the car a lot of the smoothness and power and but you will be blaming it on your engine, if you don't know.