I'll start my reply by saying that Naruto could not sense Kakashi's chakra... maybe its because Kakashi's chakra level is so Low... that the Nature-Infused Kunai of Minato overpowers it.... Basically making a camoflage to Naruto's ability.
I think that being able to sense Natural Energy, is key to the kunai...
1. The kunai are summoned, look at Kakashi Gaiden... Minato summons exactly 2 kunai per ninja there, one for each had.
2. I think those Kunai are sitting in Frog Mountain, just like Naruto's clone were. Except that the kunai have Nature-Chakra sealed and fused into the blade... similar to Shikamaru's technique to trap Kakuzo and Hidan.
The speed of Minato's flashstep is impressive... way faster than the speed that Naruto intercepted the attack on Tsunade. But I think they are connected.
1. Remember when Naruto was learning the Sage-Katas? He was bouncing mid air to fight Fukusaku. This had to be done in some manner! I think it was because Naruto was able to create a burst of Nature & Wind chakra at his feet.
2. Remember when Naruto and Sakura first saw Sasuke in shippuden? Sasuke did a pathetic version of Minato's flashstep. BUT he moved at incredible speed. Kakashi taught him to move that quickly to complete chidori.
3. WHICH means that Kakashi had to have learned how to move at great Speeds, most likely from his teacher... MINATO... !
4. If the benefit of Nature energy is to make techniques stronger, including taijutsu (ie Frog-Katas)... speed is essential.
The flashstep could be done like this...
1. Sense the nature energy kunai, and use it as a beacon. This is so that he can travel over great distances in his technique, and not come out of his slipsteam lodged in a rock, because he couldn't wrap wind around him again if he is lodged in a phsyical object.
2. I mentioned the slipsteam... Minato used Wind chakra... so... imaging chakra rubbing against eachother, to make it sharp. What if he did that with his whole body? He could draw in Nature energy from infront of him... condense it using wind chakra... thus creating a vacume-like effect, pulling him in a direction. Then use blast out the wind-nature chakra behind you for a super fast boost in speed...
3. If you are already fast to begin with... imagine with Nature chakra... Imagine Sasuke using Nature chakra to increase his speed... that would be close to Minato level...
The key to this is RASENGAN... this is a jutsu Minato couldn't complete, but he could complete this "Yellow Flash-step"???? I think these are related.
1. When creating rasengan, imagine the chakra being gathered... pulled into a central point, and then condensed...
2. Naruto's rasengan has 4 chakra streams that swirl around rasengan... but Jiraiya's did not... Naruto completed Rasengan because he thought out of the box... but what is "in the box"?
3. Rasengan would require starting with amazing chakra control at a small level. Then condensing it in equal proportions to the increase in power, and rotation...
4. Minato discovered rasengan by further expanding his flash-step. Similar to how Sasuke is expanding his chidori ability.
5. Imagine the intense amount of chakra that Naruto creates, that he needs clones to make up for his lack of chakra control. If Naruto used rasengan if made a big explosion, even bigger with wind!
6. Imagine the ROOT technique used to create rasengan... the flash-step... which I say requires the pulling in of chakra, but in the case of flash-step, it would be WIND and NATURE chakra pulling and pushing him wherever he wants to go.