When I shortened my 5-spd shifter, I removed the rod and replaced it with a (shorter) metric bolt. See photo below.
If you have access to a welder, it's pretty easy to do.
Edit to add: another option would be to shorten the top of the stock shifter arm, then re-thread it using a thread tap. You would just need to be careful not to cut it so short that the shifter knob can't thread onto it all the way.
[This message has been edited by Blacktree (edited 10-02-2013).]