PART 2 Naruto (At the first few episodes, how he was fighting Kakashi with Sakura) with no Kyuubi
vs
PART 1 Sasuke (When he just unlocked the third tomoe in the fight) without the curse mark
Taijutsu isn't a competition, Sasuke for sure wins and clones have never been an issue for him but Naruto at this juncture has countless times more amounts of chakra. At best Sasuke has 3 Chidoris. I'd still go with Sasuke though.
Part 1 Narutowas handling Sasuke's taijutsu pretty well, during the time skip his taijutsu increased a ton to the point that his clothes were torn to pieces. Naruto can use Oodama Rasengan which destroys Chidori. Naruto has better control over his summoning jutsu and easily summon a toad on top of Sasuke killing him. Naruto and Sakura made Kakashi have to use his Sharingan and he had a stronger Sharingan than part 1 Sasuke; Naruto even said Kakashi has a strong Sharingan and he was comparing part 1 Sasuke since he knew nothing about Shippuden Sasuke at that point.
Naruto's timing and usage of his clones is much better and he can summon 20 clones that all attack Sasuke from all directions. Naruto was using 200 clones while training to add wind to his Rasengan so he can spam Rasengan's or even Oodama Rasengan's with 10-20 clones. Naruto have more knowledge about fighting Sasuke in part one since he already done it and unlike in part 1, in this vs he won't have to fight handicap and try not to kill Sasuke.
Naruto also can access more of Kurama's chakra and can control up to 3 tails version 1. Going with Naruto's stronger body, initial chakra mode would enhanced Naruto's already increased stats. If Naruto was already a equal match to Sasuke when he was 13 then he would be more than a match when he's 16. Also he's better at making strategies as it was his plan that beat Kakashi in the bell test.