You can get more horsepower out of these motors, but it is going to be pricey at this early stage of R&D and current aftermarket solutions for this bike.
If you are serious about more hp, then contact a reputable piston manufacturer, such as JE, or CP pistons about custom pistons. Bumping up the compression to around 12.5:1 will gain you about 8-10 hp over stock. Any more compression and you will have to run a mix of 50/50 race gas and pump gas. Not a great idea if you run out of fuel on the road.
Porting and polishing the heads will gain you some hp too. Be very careful with who you chose to port the heads. You get what you pay for with P&P the heads, it is not as simple as a head for a car. Boring the the throttle bodies adds hp too, but changes the throttle response at lower rpm ranges.
Changing the cam profile will add hp, but you will gain the hp in different areas of the powerband, so it must be tailored correctly to function with the rest of the mods, (i.e larger throttle bodies, etc.)
You will have to have some kind of adjustable fuel controller, and build your own map for that system.
A good free flowing exhaust is a must as well. You can have the best parts in the world, but if the combination is not correct, you will not be happy. You must know what you are doing, and what exactly you want in order to have a reliable, fast motor.
With the aforementioned mods, you can reach around the 100 hp benchmark.
Just remember, with all inline 4 cylinder Yamaha engines, the crank is the weak link. The #2 cylinder is usually the one to grenade, and usually the rod snaps. Anytime you add more compression, it adds more heat, and more stress on the bottom end.
This is a very reliable engine, and it is as advertised, 'a de-tuned R6 motor'. You just have to kind of undo what Yamaha created with their de-tuning. Unless you have some connections, it may cost you a pretty penny.
Pistons x4= $225 each
Polish and porting= $400-1800, depending on who does it
Boring throttle bodies= $800
Exhaust=$800
Cams= $200 each
Controller=$350
Now you need to upgrade the suspension, and the brakes to handle the additional power. The stock rear tire will be too narrow to handle a rider that can use all this new hp all the time, and swingarm to tire clearance becomes a problem too. That is a whole another issue.
When all is said and done, you will have more in it than a traditional supersport bike sells for out the door.
Can it be done? YES! My motor is full of prototype experimentation, and so far, so good. But the bike has limitations outside of my new hp. It works perfectly for where and how I ride it, (mostly street, some closed course drag racing). I rarely get to use all the hp on motor alone, nor do I need it. JMHO