I used a pick and sharpy to mark the intake turbine, than over the nut and to the shaft prior to taking everythin apart. This will ensure that you reassemble them balanced. This is assuming they were properly balanced to begin with and you dont have to replace anything such as the turbine. In which case your going to need balancing.
people make a big deal of these rebuilds. Yes its very important to be careful and its not something to half a$$ but its definately something that saves money and i have never had a problem on all the cars i have tried this on.
In 97 i did a Talon that still runs well to this day.I did my brothers GMC Typhoon, an S4 and a few more cars.

 

mbv

 

It is important to know the intake nut is reverse thread and use lock tight when putting back on. I can post pics