thanks. Now I know I can stop wasting my time.If you missed Mukumuku in Kyaro, he won't show up again until all the other squirrels can be encountered. That's around two-thirds of the way through the game, when the Greenhill liberation arc starts. If you've only just arrived in Two River the first time, you have a fair bit of the story to cover before they'll show up.
I know it's kind of sad, but I actually started the game over just to get him early. I still have my other save file, but I just like the little guy too much to want to wait that long. To be fair, he's not the only character I want. I didn't get Anita during the Muse Ark, and I hear she has the Falcon Rune. For some reason, watching Valerie use it in the previous game was just satisfying, watching her strike a hundred blows into a large boss.