I am in the process of doing this conversion right now and since tou have the wiring harness go ahead and change it. If you plan on using your gt transmission you dont need the axle shaft but you will have to send your gtp pcm in to be tuned for the 3.29 gears. If you need any help with this just shoot me a pm and I will give you my number.
ideally you'd keep the GT transmission and drop the L67 in.
3.29's make boost more fun.