Why would you think your timing is off?Vanos repair/replacement has nothing to do with physical timing changes. The chain shuldn't be touched during the process.
What exactly is going on which makes you believe the timing is off?
Did you check the timing? Set your crank TDC (top dead center) and look at your cams, look at the end of cams, Are they parallel to each other?
Its a bit hard to explain over the net, but I personally have set timing on M54s without any special tools , just a bevel edge square. I replaced the head on M54 and put different cams(Yes, I even replaced cams without the locking BS fixture, there are tricks to that), car ran superb first start(it actually ran very well, and shaved off a second off cars time, but thats another story). No special tools were used. Nor were they needed.
Before you do anything, you need to make sure its your timing that off. Invest in a diagnostic software, your dealer visit was an experience you dont want to live through again. Read the codes and see whats going on first.
If you REALLY think you need to re-time your car, there are plenty of webpages that'll show you how to do that ,as I cant type that much, without any special tools.
Any questions, you;re more then welcome to ask , I'll try my very best to help you.