You'll want to consider putting defense enhancements in Train Ninjas. Doing so increases the dodge bonus they get along with the upgrade. You can also put Panacea in Kuji In Zen for a chance to proc during their heal.
Not sure why Oni takes knockback enhancements, none of his powers seem to have any kind of knock up down or sideways effect. I recommend changing Explosive Strike to the EoTM defense bonus. You need as much defense as you can get with Ninjas.
Try to slot SMoS in pairs for multiple hits of that sweet 15% recharge bonus.
Personally I only use the bow attacks for the 3% crit chance. I hardly ever slot my attacks for high damage.
There's no reason to put Zephyr in Combat jumping. I assume you meant to put those in Super Jumping? Also for the Winter's Gift you are better off switching to the slow resist.
I would try to get the minions and upgrades as early as possible. They are a major source of your damage/survivability.
Vengeance won't activate on minion death. I don't know if you plan on teaming a lot, but at least it's good as a LoTG mule.
Never been a huge fan of Power Boost. The extremely limited uptime means I only use it if the sets has longer duration buffs like Cold, FF or Time.
Not a fan of sleep. I'd put only an accuracy enh in Poison Gas Arrow and just use it for the -damage.
According to a quick bit of napkin match, it's possible to reach defense softcap. Buffed Train Ninjas (~10%) + enhancements (10%) + Maneuvres (~4%) + Grant Invisibility (~3%) + Flash Arrow (~17%). About 44%, but with musculature radial you can inch over the finish line.