Absolutely, take it to the dealer and get your concerns documented. Keep taking it back until it's right, if you hole a piston you're going to want a mile long paper trail showing you had concerns while the bike is/was under the warranty period and you attempted to get them addressed.
This may seem obvious and you may have already done it but scour the web for something on this. There's gotta be a ton of forums and boads devoted to this bike. Those things can be a great source of info on quirky or unusual problems. That was my experience with a site for Suzukis and also Honda V4s.
Obviously, you should take it to the dealer and have it thoroughly checked. I also remember reading somewhere that the Hondas have an exhaust valve in the exhaust system (i.e. not the valve in the cylynder head) that can make a noise similar to this. You should be able to find something by web surfing.
Taking it to the dealer and documenting it, is a great first step. Put the reponsability on Honda's shoulder, not your pocketbook! In the meantime... you might wish to check-out products that contain "Duralt", which is often used for storing fuel for long periods of time, as this usually lowers detonation problems on certain motorcycles, cleans out some carbon deposits, and increases fuel octane slightly. You should be able to find info in the web on this product, including www.duralt.com. Some persons also swear by Marvel Mystery Oil, but I have no experience with this product on Motorcycles, nor do I know if the use of either of these products will void the warranty!
The response by MO was very appropriate. Simply put its nothing that you are doing. I have ridden a few friend's CBR1000rr's and haven't heard of this problem with them. I must agree with the comments about an incredible rush though . Bottom line is its not ur fault, and I'd start documenting the problem and place it at the feet of Honda to fix. As you said you paid 10 grand, go get your money's worth.
PS I've never had a problem running my bikes on 87 octane anyways. The only problem per se is that on my ninja 250 the carbs got gummed up a lot more often on 87 but its carb was sensitive. I had a race cbr600f4 with everything done to it ported, carb jet kit, perf cam, exhaust, and intake and it ran just fine with 87 so I'm not a believer in running 100 octane or even 93.
I can't comment too much because I haven't heard the engine but I would think that it is unlikely the problem is detonation. Gasoline engines operating in that realm don't seem to do so for long... I think that the symptoms would be caused by an excessively lean mixture or an ignition timing problem. I suppose a "burr" (glow plug effect) in a combustion chamber could cause this but would think that and a mechanical inspection, beyond checking the compression ratio/balance, should be done only if the mixture/ignition checks out. I definitely agree with the advice of taking it to the dealer and carefully documenting both the problem and their reponse. Don't lose that paperwork! My 2 cents, good luck.
The exhaust valve that Hondas have (at least in the '03 954) is a single click that is audible once as you pass 3k rpm's. Yeah, it sounds like that click/ping noise, but it's not repetitive. It's simply the sound a metal flap would make opening up inside of a metal exhaust pipe. IMO, I don't think that's a possibility. I'm not much a fan of Hondas, though, so I've never really kept up with quirks on their recent lineup.