So...
The MC dies in his world and gets reborn as Kimimaro from Naruto without his illness.
Instead of joining Orochimaru he gets found by Zabuza early on in his life and he joins him alongside Haku.
(There are a lot of ways you can write this story in when it comes to plotline)
Zabuza trains Kimimaro in his Taijutsu and silent killing making him a dangerous assassin.
(It would also be cool if you keep Kimimaro's Curse mark transformation without the actual curse mark)
During the wave mission after Zabuza loses to Kakashi, he persuaded Zabuza to give up his life on the run and join Konoha.
(You can write in a different way this is just my version of the idea)
After they slaughter Gatos men and free the land of water from their misery they travel back to Konoha along with Team 7.
Hiruzen accepts them.
From here on out there are a few ways you can go... Kimimaro could join the ANBU, or you could have him join the chunin exams.