With a car this age, you have to confirm flywheel condition as it will be part of the equation. The dual mass flywheels have a definite tendency for failure and cost a pretty penny.
Changing to a single mass flywheel will make a big difference in driveability.
I recently changed my setup on a 2005 330i to a clutch masters setup using their aluminum flywheel and I am VERY happy.
That being said, I think that the Aluminum flywheel is a little too light and would recommend the steel version. You can get very good deals from resellers who will have CM drop ship to your door.
Given your M54 with six speed, most of the kits out there do not fit your car. Be very careful while shopping :-)
If you have any questions, I would be happy to answer them because I did lots of research before making my final selection.