Can a monk use Stunning Fist, Gorgon's Fist, or Scorpion Style in conjunction with Medusa's Wrath while using Flurry of Blows to get two extra attacks?
Now, the whole point of using Medusa's Wrath is so you make first make any attack that will stun, daze, paralyze, or stagger your opponent, so you gain two extra attacks while they are in that weakened state. One of the ways to achieve this is by using a Scorpion Style's strike, followed by a Gorgon's Fist's strike, then using a full-round action to perform a flurry of blows. Since the target is staggered by Gorgon's Fist, you gain the two extra attacks from Medusa's Wrath.
Stunning Fist can be used whenever you make an unarmed attack, be it from a standard action, an attack of opportunity, or any of the attacks during a full-round action or flurry of blows.
Notice how all other feats say "you deal damage normally", meaning that you can use a Stunning Fist during a Scorpion Style's strike, during a Gorgon's Fist, or during any of the attacks of your flurry of blows or even the extra attacks granted by Medusa's Wrath. Scorpion Style and Gorgon's Fist simply allow you to spend standard actions to increase the chances of applying Medusa's Wrath, even if you no longer have Stunning Fist uses left for the day.
Note that this is simply the easiest way to obtain the extra attacks, not the only way available. For instance, the Staggering Fist feat will allow you to cause the staggered condition for one round to a foe hit by your unarmed attacks. Dazing Fist will do the same, but apply the dazed condition instead.