You didn't need to remove the allen bolts, just the center bolt.
There's a Porsche tool that is used to hold the crank still while you loosen and torque the center bolt. Some folks make their own DIY version. Or you can do it w/ a impact wrench and not mess w/ this.
http://forums.rennlist.com/rennforums/964-forum/523624-crank-pulley-removal-tool.html
The piece rsscotty posted is the second part of the process. It is used in the center hole after you remove the big bolt. It will pop the pulley off the crank because the nose of the crank has a taper, so it's a pressed fit.
The crank and pulley (harmonic balancer really) have a reference pin, so if you're reusing the stock component, you wouldn't need to mark Z1 TDC.
As far as messing up the motor's balance by deleting the harmonic balancer, well... that's an unknown. Unlike the 964, the 993 didn't run a harmonic balancer. Many folks successfully run the Clewett Engineering serpentine belt kit on their 964, and that kit deletes the harmonic balancer.