Alright, so i've been experimenting more in the lab against scorpion and i found some interesting things to note:
You cannot b.3 on scorpion's wakeup after a normal command grab, air throw or charge. From what i've found, it only works from a sweep, double punch or venom uppercut.
If you end the combo in a MB command grab, you can do b.3 immediately and it is the perfect timing for it to hit.
Charge setups ie b2,3 1, 113, charge and setups similar to that do not work on scorpion. A incredibly strange event occurs, The game acts like scorpion is infront of you, where you are charging and where he wokeup but the game considers scorpion's hurt box blocking. So Raging Charge looks like it's blocked but scorpion isn't there and you get hit.
If you block a teleport punch you can stand 1, or air throw as a reversal and it hits him everytime.
You can beat flip kick as deadman said with a body splash, but it has to be timed early or it will trade or lose.
If i find anything else i'll let you guys know