Go to the drag strip. Make a run. View the replay. Use the pause button as you hit 60mph or 100kph. You can get a pretty close time that way. Maybe not perfect, but darned close.
The tools available now don't allow you to do much with the car beyond the power and weight. You can't change tire width, track, CG, etc on the car. LFS will come pretty close for basic acceleration, but not much more than that because the cars in LFS are too different from the car you are trying to model. That doesn't mean that LFS is wrong, it means that it does a good job of simulating.
Also, to get a better feel for it, google the E46 and get gear ratios and diff gearing numbers. That will help a lot. Also, because of the turbo, the torque curve is totally wrong so this will only be a very rough estimation. I understand doing it though... it is fun
I also think the weight you listed is a bit low. It should be closer to 3200lbs. My E46 323i is about 3150 without fuel or driver.