I cut my shifter... about 1.5".
I first had a B&M short shift adapter on the stock shifter... made a pretty big difference in the throw of the shifter... which made for slightly faster shifts... but not good enough for me yet. (note: dont pay $75 for the B&M adapter, get the generic ones on ebay, same thing!)
I took the shifter out of the car, cut at the stock weld point... and grinded off the old weld... I cut the shaft down to where I thought would be good (about 1.5") and rewelded it to the base. You cannot cut the top of the shifter off, the shift shaft is hollow and you WILL NOT be able to re-thread it.
Overall I was very pleased with the shortness... but I still wanted more... so I took the tenzo type-R knob off and replaced it with a WRX/momo leather knob I bought from Subaru ($82), which is threaded all the way to the top of the knob, so it sits lower on the shaft and again, shortens the throw and length of the shaft. Now I am happy.
The WRX knob was not a direct fit, as the threads are larger in that knob, so I used a threaded insert on the shaft, and then threaded the knob onto that to make for a tight fit.