I would say the best way to do pain is simply make 6 different characters, all specializing in one specific thing; the summon one obviously being a constructor/ectopic adept. Apparently those dog things explode now, they didn't really show that in the manga, so I would make them the carapace one that explodes, the flying egg bomb one would be something like the flight ability and concussion blast, the chameleon has natural invisibility, etc.
So then rinnegan is detect psionics at-will, and maybe favored energy or what it's called for five different energy types for all the seven bodies. What could simulate Human Path and Naraka Path's ripping people's souls out deal. The body that absorbs ninjutsu and chakra could be using psychic vampire (though the ninjutsu absorption i dunno what that would be).
Oh, and Forced Sense Link between the seven since they all share their fields of vision.
I would say that the Naraka path should be obvious...its urge extermination, it kills people instantly.
I would say the ninjutsu absorbtion would be something like tower of iron will (for half damage), combined with a vigor and dampen power...or something like that.
You reduce the power to its lowest damage with dampen power, your tower of iron will reduces that to half, then your vigor absorbs the rest of the damage, which should be very little.
Either that or it could simply be a null-psionics field.
I also disagree that the susanoo bone cage thing, or susanoo itself is a mere skin of the construct. That's far too weak to cover for the massive amount of damage it can resist. Susanoo is supposed to be an absolute defense.
I would also like to address a couple concerns I had about the general ninja powers.
Kawarimi - I think this ability is so integral to ninjaing that the power you had listed for it before is inadequate for what it actually accomplishes. A kawarimi is used in order to essentially negate an attack used on the defending ninja. This eludes to the fact that it is an immediate action ability and Dimension Swap does not fill that requirement. It is my belief that the Kawarimi (and its ilk; using a clone) is so important to ninja battles they simply wouldn't be the same without it. Like the kawarimi, battles in dungeons and dragons were forever changed by the introduction of swift/immediate actions. The ability to instantaneously negate an attack no matter how powerful that attack is seems more akin to what the kawarimi is supposed to be.
Therefore, I submit that the kawarimi technique should be one (or any/all) of the following.
Evade Attack (augmented)
Schismed or quickened (or both) synchronicity every round which can be used to dimension door (or even swap) away from an enemy attack.
Anticipatory Strike