The using to much chakra for a jutsu was because of kuramas chakra interfering with his chakra levels which was stated in part 1 which has been overcome because of training and becoming friends with kurama.
rasengan required releasing pure chakra into the physical world and maintaining it's shape and flow which requires high chakra control. For the element control he had to maintain a rasengan while adding wind chakra to it in the right levels or it would blow up in his face as we saw. As for the clones he divided his chakra hundreds of times and had them making rasengans and using wind element without the kyuubis chakra as it was surppresed so he had to be careful with his control or he could have died.
As for yin seal I agree that it's impressive (even if i don't agree with how she got it) but it still took her three years to do what Tsunade can do in a matter of days. It's storing chakra in ones body which is the same as sage mode except sage mode requires a user to store nature chakra in ones body which is harder to control.
Finally Naruto can manipulate Kuramas chakra and shape it to meet anyones and not have it harm them then, change it in seconds to meet someone elses a more dificult feat then storing and controlling ones own chakra
Well said.
As I said, Rasengan is the ultimate shape manipulation. As we saw, it does take control of s high level, and this is why Naruto uses clones... Because his is not perfect... Though not to say is not impressive (as it.is impressive).
Shadow clones are a jutsu in which half of one's chakra is absorbed into a manifested clone...increasing the clones simply increases the divisions of chakra whether everyone gets 1/2, 1/16, or 1/100th. Once again adding Nature transformation is impressive, but once again due to his lack of mastery over control he needed to have yet another clone to do shape and one to do nature.
Kurama's chakra has definitely been a good improvement (especially linking), but once again we must analyze just HOW MUCH chakra Kurama has....and that answer is REDICULOUS AMOUNTS of it. As such, Naruto is able to use his rasengan and Rasenshuriken without Clones because his overwhelming chakra supply gives him the amount needed to disperse the shape control and nature transformation to where their sheer presence can allow him to force the balance.
Comparatively, the Yin Seal requires absolute precision with minimal room for error or else one isn't storing chakra. Additionally medical ninjutsu requires perfect control as the nature of it involves working on people. As such you must manipulate your chakra in ways that will do some of the following:
1. Relieve only so much pain
2. Cut only so deep
3. Reform only so many cells
4. Insert this much chakra to stop the bleeding
5 use this much chakra to maintain a bubble while using chakra to insert it into the body. Then it must use even mire chakra to capture/detain/identify/remove poisonsr infected cells from regular ones.
While I'd say for sure mastering Shape and Nature transformations show great skill in controlling chakra, the true mastery of chakra comes from committing the perfect and precise amounts of chakra in exactly the ways they are supposed to be. In that regard I find Sakura's medical ninjutsu more precise, and as such it sways my judgement in favor of her.
But regardless Naruto definitely has great levels of chakra understanding/control.