If you're going to give him a Kekkei Genkai or Bloodline Limit, why not go for OP as Fk and give him a pair of eyes identical to Kaguya's third eye? That way he'll have all five main elements and be able to copy jutsu like the Sharingan can allowing him to be able to copy techniques like Haku's Demonic Mirroring Ice Crystals or "Crystal Ice Mirror Jutsu"? On the other hand if he had the Dust Release he'd practically de-atomize anyone including Logia users like that Rabid Dog Akainu, and the slayer of Shipmates "Blackbeard". Although there is something I find highly amusing in all honesty. One Piece's Edward Newgate aka "Whitebeard" doesn't have a beard yet he's called Whitebeard, what, the only facial hair he has is his crescent shaped mustache.

Rinnegan-5-6 My vote This one is a good choice as well control over all of the elements as well as life-and-death And creation of all things though it is nothing like its predecessor having all bloodlines it is a very close 2nd hand as also a combination Of 2 clans

Rinnesharingan-1-2 If he gets this one he will have every bloodline So this one is pretty much an all of above choice Anyway keep up the good work

I don't know if you've noticed or not but in the first chapter you head Naruto meet the Kyubi for these first time after being knocked out in a mob beating and in this chapter you had him meet her for there first time after passing out due to pain.
You might want decide which is the real first meeting.

rinnegan and iron release

Kyubi could be physically 10-12, is actually thousands of years old or you could do like in the fanfic Naruto's Kit where every time a Biju is killed they are reborn, like a Phoenix, into a toltally new life with only very vague memories of their past life.

4 on sand control and 3 on rinnegan

...some grammar issues and at points it feels rushed

rinnesharingan, yin-yang release and dead bone pulse. you should add nami and vivi to the harem.

rinnesharingan, yin-yang release and dead bone pulse. you should add nami and vivi to the harem.

Hanabi

I think you should add fem Luffy to the harem. As for the bloodlines Yin Yang,Iron Gold and Silver Sand,and Chaos.

I think you should add fem Luffy.

If you have to slim down the harem then cut Samui,Isarabi,and Fu.
As fof the bloodlines Chaos Release,All Three Sand Releases,and Yin Yang Release.

If Naruto is going to have a doujutsu, please make it the Rinnegan.
If he is going to have any other bloodline one of its elements needs to be at least wind type as that has always been his major element alignment. So either Storm and/or Hurricane would suit, but Hyoton? (Ice Release) could work too. I've also been kind of partial to Naruto unlocking the Addimantium Chains.
As far as the third fruit goes, if I may make a suggestion, Mystical Zoan Type: Kaiju-Kaiju : sub-class - Gojira.

No fem haku