I want to take the fire effect shader (the one for fire damage) and do two things: firstly,I want to turn it upside down, so it flows towards the ground
This is easily done, Initial Velocity and Acceleration all 6 of those inputs relate to world axis X,Y and Z so positive values will make the particles go Up and Neg will go http://www.youtube.com/watch?v=5EPi10Z-hnM, Spell I created that uses downward moving Effect Shader particles.
secondly, I want to edit it so that it's point of origin is the Player's waist-- so it looks like the effect shader is flowing out of the character's body, and creating a kind of "wave" for them to ride upon-- is this possible?
No, Effect Shader Membrane applies to the entire model its being used on with the optional flag of effecting Skin Only but still effects the entire model -> and the Particle portion the Particle Emitters are bones every bone in the objects scene so its impossible to only apply the particles to the waist.
You can try to make the particle start small enough so that they are inside of the mesh until they reach near the waist but particle are generated in World Space so they will not follow the actor they are being generated from so even the slightest movement and everything will be seen.