I aligned mines from the bottom up, that is, starting from right above the d-pad and working slowly upward towards the ear piece at the top of the phone. Keyword here being, "SLOW". Not trying to dismiss anyone else's experience, but mines was a rather 'painless' one. No trapped dust particles, no air bubbles, no misalignment.
But then again, I braved this process only AFTER having read this thread @ PPCGeeks. So maybe thats what made all the difference.