Yeah, that was a really good writeup. The ninjitsu package itself should have an emphasis on defensive maneuvers; ninjas were generally not supposed to go toe-to-toe with their adversaries if it could be avoided. The emphasis would be on breaking contact and escaping, possibly after a disabling nerve strike.
If you want a more mythical ninja, you could start adding in alchemical and gadgeteering skills; ninjas were famous for poisons, smoke bombs, traps, water-walking and underwater breathing devices, climbing apparatuses, and so on.