Yeah that is a cool video . Yeah I should not get complacent . Just keep practicing . Do you need the block off for the air if you get a pc5
Stick with the R3 for a little bit, especially if you are starting to do track days. You will learn much faster and much better (less bad habits) on the smaller bike. It forces you to be precise and smooth because mistakes get amplified. Its also is easier to learn, push yourself, and feel the edge of what's possible on a lighter bike, you feel more feedback and learn your limits better. Plus, the corners come at you slower, so you have more time to think, plan, set your entry speed, and ultimately, you'll end up cornering faster. I started doing track days and racing on a CBR1000, then borrowed a friend's 600 and did faster lap times on it so I upgraded to an R6 and got much better, then I upgraded to an R3 and now I'm really honing my skills. Plus it's wicked fun to rip around the outside of people in the corner who are on bigger bikes.
As for the fueling and exhaust questions. CapitalView is right, if you want to get better, spend your money on other things rather than a few horsepower. However, if you changed the exhaust and you're noticing the downside in performance and the popping from backfiring, a fuel controller will fix that, and help the bike run better. The R3 is unique in that the stock exhaust really isn't as bad as a lot of bikes. Adding a fuel controller like the Bazzaz Z-Fi or PCV to the stock exhaust system produces nearly as much horsepower as tuned full systems, and adding a fuel controller to the Akrapovic slipon produces a good boost in torque and top end horsepower.
I did a full range of testing the Akrapovic exhausts with Bazzaz, you can see the results here:
http://www.yamahar3racing.com/2015/05/yamaha-r3-dyno-results-with-akrapovic-full-system-slip-on-and-stock-exhaust-tuned-with-bazzaz-zfi/
There are a lot of dyno charts there, if you look closely, you can see the Akrapovic slipon without tuning drops the performance a bit, but once the Z-Fi is added and tuned, you get a small gain in torque and a pretty decent gain in top end over stock, plus a beautiful power curve. I don't think you need an auto tuner, you won't need to be changing it all the time. The map we developed is precisely for the bike setup like yours and will be tuned very well, you can just leave it alone. For your setup and needs, both the Z-Fi and PCV will do exactly the same thing, but I would say the best bang for your buck would be the Bazzaz Z-Fi, which is a little less expensive than the PCV (I sell both), and I have a map specifically tuned for that exhaust already for the Z-fi. I'd recommend getting a Bazzaz Z-Fi and save the rest of the money for your next track day, better tires, Vesrah brake pads, etc.
Also, some of the popping on deceleration is likely coming from the air injection system. You don't need a block off plate unless you will be dyno tuning the bike. It doesn't help performance at all, it just has to be removed or bypassed to get an accurate reading from the exhaust of the air/fuel ratio for tuning. For an Akrapovic slipon, I wouldn't bother with tuning since I already have a map for that setup. But you might want to consider removing the smog system if the popping is bothering you, especially if you're moving toward tracking the bike. Here's a "how to" on that:
Anything else, feel free to ask