This is an old guide, but with Cryect's Tools being open source I'm sure you can update it to what you need. Or someone here will.
Injecting Particles
1. Open MyWarcraftStudio and extract the M2 you want to get particles from. A good way to find what model has particles is to browse threw the models in WoWModelView and enable/disable the particles on models you think have them or you like.
2. Still in MyWarcraftStudio extract the M2 you want to inject the particles into.
3. Open up Cryects pExtractor.exe and load the model you want to get the particles from. Once it's loaded the m2 it will ask for a file description. Name it whatever you like and hit enter.
4. Now open up CMD again (command prompt), type in this command: C:\pInjector.exe C:\ModelYouWantParticlesToBeIn.m2 C:\ParticleFileYouExtracted. Press enter and it will run threw some text that will look like:
You just injected particles.Code:Particle Injector V1.0 <May 29th, 2006> by John 'Cryect' Rittenhouse Loading Particle C:\ParticleFileYouExtracted Loading Model C:\ModelYouWantParticlesToBeIn.m2 Injecting Particles C:\ModelYouWantParticlesToBeIn.m2 Writing Model C:\ModelYouWantParticlesToBeIn.m2
5. Now go open up the newly injected m2 in M2Modder, go to Edit Particles (p) and then go to Position (p again).
6. Now your going to edit the position of the particles on the model. Press 0 and you will notice that its in the XYZ coord format, fill in where you want it to be on the model.
To fix the blocky particles, go back to Edit Particles, press t and enter the particle number, find the tree path of the particles and then put that tree path in.
Changing Colors
1. Open up MWS, fine the m2 you want to change the colors up. Extract.
2. Open the m2 up in M2Modder, choose Edit Particles then Color.
3. After that opens up choose the particle number. Now your only going to change the last 6 numbers. The color codes are in hex. So google is your friend. Get changin.
All done. Enjoy.
If you enjoy some hex editing there are a few things you can change in the file with particles: Emission Speed, Vertical/Horizontal Range, Gravity, Lifespan, Emission Rate, EmissionArea Length/Width, Gravity Strong. All this can be found at the wiki so check it out.