near clouds home town in the bushes or near rocket town ( after the mountain area )

You can find Yuffie at ANY point in the game, all you have to do is go into forests anywhere on the world map, fight a few battles and you should see her, after the battle, this is what you do
First she'll ask to fight again.
Say: Not Interested
-She'll start taunting you, and ask if you're scared
Say: Petrified
-Now she'll start to leave...
Say: Wait
-She'll ask if you want her to come
Say: That's right
-She'll say okay
Say: 'LETS GO'!
DO NOT ask for her name OR use the Save Point, or she will run away!

forest

anywhere at any point in the game as long as its in the forest