If you test the iPod and the click wheel is not working, try putting in the metal bracket, after putting mine in the click wheel started working again, I think that added pressure from the metal bracket is required to get the click wheel to work.
If you happen to make marks on the plastic top of the iPod especially if the marks are on the edge, you can sand down the edges with a nail file or fine sandpaper to make it look better.
If the top is bulging its probably because there is a lot of adhesive there and making it appear as if its lifting up, in my case my iPod was already opened by someone else so there was a ton of adhesive, removing it will make the top and bottom parts sit flush with the housing again.
This was a really good guide, I got my Wii working again and I am happy.
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