What you're experiencing is one of the toughest aspects of repairing the 4th gen iPod Touch. The tolerance for any irregularities in the aluminum case is very small. In other words, it doesn't take much to prevent the screen from sitting flat in the case.
The best method that I have found for reshaping the corners of the case is to use a small flat head screwdriver, and hammer. Sometimes, you can get behind the plastic bezel and make direct contact with the aluminum case, but somethings that is impossible without damaging the edge of the bezel. Otherwise, the only other way to do it is to pound the flathead screwdriver through the plastic bezel and hope that the edge of the bezel doesn't come off. Honestly, sometimes it's just impossible to avoid damaging the plastic bezel.
After doing some work on the corner, make sure you do some dry fitting before trying to put back together. You really do need to have the screen fit in pretty easily to not have problem with it sitting flat in the long run. My preferred method of dry fitting is to turn the screen over so that the back is facing upward, and then put it into the case. Just be mindful of the digitizer and LCD connectors when dry fitting this way, as they are rather very fragile and easily damaged...especially the digitizer cable. Also, make sure you remove the flimsy screen protector from the factory before dry fitting that way, as that screen protector can often be larger than the glass itself.
Hope that helps. Some others may be able to chime in with their preferred method.