When I had my psp apart, I managed to bend the little metal piece that sits under the analog stick and next to the screen, and the case wouldn't close properly.
I'm not saying that is your exact problem, but my point is, simply that you may have bent or otherwise don't have everything together properly. Even if things are in the right places, you may have warped a bracket, or not put a cable in correctly. It doesnt take much to make it all not fit together properly.
I'd go back and just triple check that everything is not bent, and possibly even look up a psp tear down guide, or watch a couple vids on youtube. Never know when you might find something you overlooked.