I may have found the problem, but I'm not sure:

Here's a photo of the WG arm attached to the flapper:
http://s132.photobucket.com/albums/q...t=IMGP0589.jpg

Now when I pulled off the cotter pin and slipped off the WG arm, it sprung out towards the radiator.

Notice in the photo how its bent out towards the radiator. Is that normal?

http://s132.photobucket.com/albums/q...t=IMGP0595.jpg

Here's a couple more photos showing the relative distance between the hole of the WG arm and the flapper shaft.
http://i132.photobucket.com/albums/q...7/IMGP0619.jpg
http://i132.photobucket.com/albums/q...7/IMGP0625.jpg

 

Do this http://store.forcedperformance.net/m...td-setting.mpg

And don't be afraid to bend the rod a bit so it doesn't bind when it moves. As I said before use a bike pump and pump a small amount of air into the hose coming from the WGA to your MBC and make sure the actuator moves smoothly.

 

Is the rod removable from the rest of the WGA? It would be a lot easier if I could remove the rod and bend it to the correct position, rather than having to unbolt the WGA from the turbo.

 

No, the rod doesn't come off but it will twist some and that may help to get it lined up better for you. From what I see you need to loosen the adjusting nut and get the end piece lined up better with the arm, while the arm is off the actuator you may as well check the preload.