The better shifting, sounds like that part of the map is dead on. I know what you mean, some tunes are perfect some feel lazy when shifting.
The popping on decel is too much fuel, the big BANG around 2000 RPM on decel, its where it goes richer igniting a bigger flame, I bet it shoots a flame right then.
The fuel mileage is because its probably running a bit rich most of the tune, but such is the cost of modifying your R3.
Lumpy tick over is almost certainly a too lean idle, trying adding fuel, like 4% to the 544 and 627 areas of 900 and 700 RPM in the L tables.
13 Seconds into this you can see that rich swing spot I'm reffering to where you're probably getting the bigger pop noise: