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[Scatty]

3 Ninjas is not very convenient, since you need at least someone to heal and someone to be able to summon higher level monsters to aid the party. Since Clerics heal AND summon, you should also have at least one of those in the party for the first stages of the game. Later, when the Ninja has developed it's fighting skills and begins to learn Alchemist spells you should begin to invest some big points in that area, all the fighting skills will develop automatically during the fights.
Seeing it that way, it's enough to have just a double-team party of Ninja and Cleric. That way they level-up even faster than three, both can fight good enough and with Cleric you have advanced healing spells that Alchemist does not and some good attack spells too. Besides, Cleric can wear divine chain armor pieces which provide good protection and regeneration, and as he's not able to hide like Ninja does, he needs all the best stuff in the game he can wear. Also, it's a good idea to have a Fairy Ninja for the obvious advantage - Cane of Corpus. Also Fairies have better armor class than others.