Ok one thing I luckily never had to touch on either E39 or E53 is the ABS module.
That being said, are we talking about coding the zcs?
It can be done with NCS expert.
If that's what you mean, it's not that hard.
Get NCS Expert, INPA and Bmwscanner installed and working on your computer.
Let's start by reading your ABS's ZCS code.
I'm not sure if it stores VIN as well and maybe VIN needs to be adjusted as well.
But even before that, you should scan your car for errors with bmwscanner to see what errors there are.
Normally whoever rebuilt or fixed your ABS module should be able to set you up so that everything works properly.
Maybe your lights are not even related to ABS.
You should provide some history to your problem.