This effects pack should be used as an external library, to prevent changes to the originals.
In your .fla, go to Import > Open External Library, and browse to the 'FlowEffectsPack.fla'.
Drag over the effects you want to use:

Make sure you drag over the effect MCs and not the whole folder. Generally you will not need to access the 'assets' folder directly. It contains the elements of the effects, and are added automatically.
After dragging an effect into the library, you can instantiate it just like any mc. Add a linkage ID, and use something like:
var mc:MovieClip=this.createEmptyMovieClip('mc',this.getNextHighestDepth());
mc.attachMovie('flowID','flow1',this.getNextHighestDepth());
Depending on the clips registration, you may need to move it after attaching.
Similar to the AS2 method:
var flowMc:flowLinkageName=new flowLinkageName();
addChild(flowMc);
Within each effect's MovieClip, there is a container clip with effects/transforms, etc added to it. You can modify this effect list to give a completely new look.
You can edit the default particle (a circle) in each effect. In the 'assets' folder in the library, there are 'particles' corresponding to each effect ('flow_01_a' for example). You can edit these graphics to customize. You can even place an animated MovieClip within the particle graphic, which opens up whole new possibilities.
In the 'FlowEffectsPack.fla', look in assets/source SWFs for the looped versions of each. To easily substitute these into the original effects (flow_01, for example), just edit the clip, and swap out the .swf. The effects/transforms, etc will be preserved.
Find the source for your effect ('flow-01.swf' for example), select the frames, and right click > Reverse Frames.
(Make sure you delete the bottom layer of the source swf of your effect. This is used as a placeholder, and will be used as the masked area if not deleted.)
Since these effects are timeline based, to speed up an effect, just remove every Nth frame. So, for half speed, delete every other one.
To do this quickly: > to shift over one, then Shift+F5to delete the frame.