Have you or anyone else ever experimented with cams? I would think that would be where the power is to be found, especially with an intake cam.
Cams are available, but, IMO are more of a race only item. My reasoning goes like this. I believe that Yamaha did a good job of choosing cams that would give good midrange and topend power for the Apex's intended purpose. Which is good trail performance. And given its weight, they felt it needed good midrange power. They had to be conscience of engine rpm and belt speed to give adequate longevity. IMO the Apex is in a fairly mild state of tune. Conservative fuel maps, and timing, and reasonable rpm. For the guys who dump crap gas in their machines and then go out and hold them wide open for miles. The factories don't like warranty claims, and they don't like unhappy owners trashing their product.
Would hotter cams give more power? Most likely, but, they would in all likelihood push the rpm's higher in the process and lose that all important midrange power. And now the belt speed is reaching even higher inefficient speeds without even further reduction.
Already been through this scenario with my street going Kawi ZRX12oo. The stock cams give great low and midrange power, but, sign off quickly at about 8,500rpm. Very low by todays standards. So when I did put a hotter set of cams in it, guess what; more power, but higher up the rev range, and a predictable loss of midrange. Bikes can get away with turning more rpm as long as the engine can take it. They don't live at redline like sleds do, and they don't have to worry about driveline speed.
An Apex is already close to making its peak power near rev limiter cut in. So you don't have a great deal of rpm to play with, maybe 800rpm at best before the limiter cuts in at about 11,200. So right about the time the better power is coming into play, guess what, end of party. Now can you eliminate or raise the limit? Probably, but your still stressing the engine more and pushing belt speed higher in the process.
All of these things can be overcome, but, at what cost, and with how much work? Its much cheaper and easier to get better performance through a power adder, and keep the belt speed and engine rpm at or near stock levels.