So, if you have completed the game and have NOT received the Game Master award because of the technical glitch that skips the 100% mark all you have to do (and I tried this to make sure it works) is:
Go to the PAUSE menu and select New game (duh, make sure you saved your game at 100.96%) and when it asks you to enter your name, enter HCRAYERT ( the classic cheat everyone knows). Leave the PAUSE menu and you will start Chapter 17 "The second day of the rest of your life" BUT you will not lose your achievement awards.
You WILL lose your Swing Speed level 7 and 8 and be reduced to 96% or something similar. Go to the Spidey Store and purchase Swing Speed 7 and 8 (and you may as well purchase everything else missing), leave the Spidey Store and WALA! You will acheive 99.99% and be awarded Game Master. Then you can rest knowing you're truly conquered the game.