Yesterday I dabbled in making my own Shimeji, or little desktop pet. Specifically using shimeji-ee to make stupid ittle Ingrid babies swarm my desktop. As I write this, they torment my screen as we speak.

During this process, there was a question I wanted to find the answer to, couldn't find, but was able to track the answer down myself relatively quickly. Typically, a Shimeji's idle is just one frame, but I wanted Stupid Ingrid Baby to flap her little arms around. So here's how I acomplished that and how you can change the specific number/speed of animation frames for certain actions for your shimeji.
So first, assuming you already have shimeji-ee and java installed and the sprites you want to use formatted and ready to go, head to the shimeji files, open the file labeled comf and from that file, open actions into notepad or whatever you use to edit the code.

From there, you will find the pose frames associated with each action (ex: "< Pose Image="/shime1.png" ImageAnchor="64,128" Velocity="0,0" Duration="350" / >" under the action for standing). So simply replace the image (ex: shime1.png -> ingrid1.png), copy and paste the code with the different frames for the amount of frames needed (ex: ingrid flapping her arms is two frames, so under the ingrid1 code, put another but with the image as ingrid2, etc), and for each, change the duration for the animation speed (ex: lower numbers = faster speed, i have ingrid's set at 4 for her flapping). I reccomend keeping the duration and image anchor numbers the same as they are listed by default on each different action.
Now you know! Now you can have shimejis blink or if they have an intricate 45 frame walking animation, now you can add it!