The thing is YK scored 10k runs, whereas Pujara has 5k runs. You are underrating longevity here. In order for Pujara to overtake YK, he would need to get close to 10k at a 50+ average. With 5 years of test cricket left in him (he does have a dodgy knee, so it might not even go to 5 years) with 2-3 years of peak, I dont think he will get close to 10k.
As for SENA countries, YK is still ahead, in terms of important innings and averages.
In England, YK does have the 200, which puts YK ahead in England.
In SA, both have very similar with both contributing in important wins.
In NZ, Pujara has played only 2 tests, but YK is significantly ahead.
In Aus, Pujara is way way ahead after this series. It does make up a bit for the failures in England and NZ, but not by that much.
If Pujara can have a god NZ series, and have another important innings in England and score 10k @50+, then I would agree that he has overtaken YK. But that is very far from happening.