but after using only 3 of those 1000, his stamina gives.... I still think kakashi's up there, but what about Darui?
I'n not sure why people still decide to ridicule Kakashi's chakra/stamina reserves.
Kakashi's chakra capacity (either that, or his ability to use jutsu with enough precision to not use as much chakra) has increased substantially. When we first seen him, he'd pass out after just using a Mizubushin, and 2 Suiton ninjutsu with the Sharingan active.
Fast foward to his battle with Kakazu:
Kakashi used 6 Raikiri I believe Suiton: Suijinheki and intended Mangekyō Sharingan usage (granted, he would have ended up in the hospital by his own admission but still) All this was the sharingan active.
And yes, Raikiri does require a large amount of chakra.
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(a lesser version of Raikiri) only can be used atleast 4 times a day(part 1 Kakashi) without killing the user (and Sasuke(part 1) 2 times). These things were established as far back as season 1 (long before Shippuuden).
Foward to his battle with Pain:
With only half his chakra(his chakra was split in half after using the Raiton Kage Bunshin) Kakashi used three Raikiri (each take up a hefty amount of chakra)(1, 2, 3 - assuming the fourth Raikiri and Raiton: Ryouken were used by his Raiton Kage Bunshin), a Doton: Moguragakure no Jutsu, a Doton: Doryūheki and one Kamui (excluding the second one that killed him)
People also forget the sharingan causes more of a strain to Kakashi's body (due to not being an Uchiha) and think he has low chakra. Kakashi is no where near as chakra/stamina handicapped as people make him out to be.
Kakashi might not have tailed beast chakra levels, but he certainly has enough for a decent fight.
@OP, I would say Kakashi. Guy is also pretty close.