You need special tools to re-install the VANOS system, that's going to cost you more than $400 by itself.
My experience with the M54 head is that unless you know what you are doing, it's best to leave it alone. Proper porting of this head involves adding material, not just grinding it out, which most have no clue about.
You don't need to helicoil or timecert the block. If you are advised to do this, the person probably doesn't know much about the M54 block. (I put VAC motorsports in this category)
Not a big fan of headers, as they make a heck of a lot of noise, and are in general a pain to install. (I'm talking about fabrication and installation of post header cats as well)
Changing to an M54B30 intake manifold has some OK gains.