Nice, those all sound like pretty solid changes. I would say look at the nunchaku at level 11+ and try to think of any way your player could exploit it before cementing it. If you run the numbers and decide that it might get a little too strong in the next 3-5 levels, maybe just pull even more influence from the staff of power, give it x charges and let those charges be usable as a scaling smite trigger. This way you can still give the player the extra smites you're aiming for, while leaving his spell slots open for more smites/spells depending on the situation. I'm not sure how many charges you'd want to put on it though.

Then again, smite damage maxes out at level 4 spell slots, so using it with a level 5 slot or higher would be inefficient unless the character has no spells capable of higher damage at those levels. So you could keep it how you have it as well. It's tough to quantify exactly how "worth it" higher slots would be since a 5th/6th slot would miss out on 1/2 dice of scaling due to the smite ability limitations, then again it nets the player a refreshed 3rd/4th spell slot. This is what makes the skill hard to fully scope out without testing it in play or spending a lot of mental math time plotting out how much they smite with higher level slots (if any).

I think the only thing I would reword a little bit would be the savage ability again, it might be because I'm still sleepy but I don't know if your clarification text is stating that natural/mage armor does or does not count as "armor" for the purposes of the ability. I am assuming you meant that they DO count as armor, but note that a wide variety of even mundane animals come equipped with natural armor (boars, wolves, bears).

I really like the theme of this ability but I'm having trouble trying to figure out if it'll proc too much or too rarely. I would say either look at the adventures you have planned, or scrape together a few encounters that you would realistically throw at the players and take a look at how many this would proc even before taking poison resist/immunity into consideration. You definitely don't want to have to constantly be asking yourself if you're picking enemies that will allow your player to make use of his weapons ability. But you also don't want him/her to feel like they got shafted and be looking to swap it out for a generic +1 rapier in the future considering the time and thought you're putting into these weapons.

It's one of those things where, when it doesn't work on something, it's worthless the whole fight. When it does work on a creature, that's double the weapons base damage on that creature the WHOLE fight (unless they cast mage armor or pick up a shield). This might need tweaking a little, but unfortunately I don't have any solid suggestions atm since I am not strongly experienced with encounter expectations at level 9+ or with the type of monsters your campaign is likely to throw at the players.

Anyway, the weapons are shaping up nicely, the wording changes and more detailed descriptions are good. Keep it up, I hope your players love them.