You can make parts of character animation in different files and mix them together in another file using the Trax Editor in Maya. Here I had my witch Liah walking, running, and idle in different files but with the same bone and controler structure.
First we want to make a character set, so select all joints and controlers that you character has. You can select the parent controler and select Edit => Select Hierachy for easier selection.
Now in the Animations tab, go to Character => Create Character Set.
Open up Window => Animatin Editors => Tras Editor. With the character set selected, go to Create => Animation Clip .
Select Time Range : Time Slider so it only animates the keys in the time slider range and hit Apply.
Now click on the animation clip so it highlights in yellow and go to File => Export Animation Clip…
Repeat the steps above for all the files (ie: walking cycle file, running cycle file, idle file).
Once all clips are exported, open up the Trax Editor in one of the files. Make sure the character set is loaded at the bottom right of the Maya window. If not, select it from the drop down triangle.
Go to File => Import Animation Clip to Characters… and select the files that you exported earlier.
The trax editor looks and behaves somewhat like video editing software. You can move the clips along the timeline by left mouse dragging the clip boxes.
To make her run cycle longer (without making it slower), shift + left mouse drag numbers along the bottom of the clip.
To make her walk slower or faster, left mouse drag numbers along the bottom of the clip.
To cut frames out, left mouse drag numbers along the top of the clip.
You can also blend animation clips by selecting two clips and firing off right mouse click => Blend