Okay, I'm going to assume you are installing this one. Not sure if there is a different one.
The upper body hinge and upper backing plate that came with mine were different than the ones I ended up needing. I have an '06 and the hinges are different. My advice is to make sure you install the tailgate hinge brackets and the upper backing plate. Then put the arm assembly on with the upper body hinge check your alignment there before anything. It should line up.
I had the pleasure of mounting and drilling everything like the instructions said only to realize I was given the YL upper body hinge and upper backing plate. So I have a couple extra holes.
I'll try to post some picture of it later if it would help. Try and post a pic of where your progress is right now.