The stock head pipes are pretty well designed for street use.
Sato low-mounts work really well with the stock head pipes.
I've never dyno'd Yoshimura slip-ons or full system. So I don't have any numbers.
Maybe others here can supply the info.
As for modifying OEM mufflers, you may develop a situation where you lose HP rather than gain. You'd have to do modifications in conjunction with dyno testing to make sure you're not wasting your time and money.
They spent a lot of dyno time to match their mid-pipes and mufflers to the stock head pipes.
The end result is a very nice power spread with a large mid-range torque increase.
That's why you pay around $900-$1100 for a set of slip-ons.
I believe it's a kit that contains the wires and connectors to perform the soft rev limiter mod.
The instructions on RC51.org explain how it's done, only you have to scrounge around for the connectors.
Since I don't race my bike, I'm perfectly happy to keep mine in place.
Although I was tempted recently when I tweaked my power commander map to match my Akrapovic system.