I had the same problem. You can get some Lv. 3 spheres from various places. The first chance you get is by stealing from the Ronso brothers, but for this you need to teach Kimahri Steal/Mug. You can also receive Lv. 3 spheres from the enemies in the Omega Ruins, but only occasionally. As for the Lv. 4 spheres, you sometimes get them from bosses near the end of the game, but the majority of these spheres are found in chests throughout the game.