If everything else is fine and all you need is a"shorter" pulley check Mike Doty's website.

http://www.dotymi.com/Automotive_Home.htm

I use the Doty pulley with the other stock pulleys and everything lines up perfectly. This is for ATI dampers though. The difference looks about the same, though so this could be your answer.

Here is one with a Doty crank pulley, stock w/p pulley.

EDIT: Looking at the pic you posted(side view) it looks like the pulley isnt seated far down enough. Is it the hub? I doubt there is anything wrong with the crankshaft...

Maybe its time to drop back and punt. Sell off that FD to someone else, get an ATI and a Doty pulley and you can use all your billet stuff. Problem solved..

MB