Can someone explain the 4500 rpm surging and how to fix it?

Correct on the replacement of the plugs, but the condition of them tells how they are firing. White, tan real lean while black, brown richer to the point of being wet.
Fumes from the exhaust also hint at rich.

With so few miles, only having issues at 4500 rpm is odd.
Running good until redline is great, does it idle low and well? Your bike has carb's or injection. With that mileage I'm guess injectors which would be really odd at one rpm.
If your in a high gear like 6th, going slow like 40mph. (RPM UNDER the 4200 rpm) If you try to accelerate do you have issues.
Might post a video, showing the issue and taking it for a ride. Only at 4500, with a carbed bike would say the needles are not the fit for the bike. Don't think I have a DYNOJET kit for the bike, had several different bikes.
 
Haven’t pulled the plugs yet but it does stumble in all gears. The rpm is always the same. I didn’t pull the spark plugs because the bike only has maybe 6000 miles on it and I think you are supposed to change the spark plugs at around 20,000 miles if I’m right? So that’s why I didn’t pull spark plugs. Above 4500 RPM all the way to redline it runs clean and pulls very strong, no stumbling at all.
Then stop wasting everyone's time. We gave you answers and you just argue like a child. GO AWAY!
 
I gave up and brought it to a shop. The guy said the spark plugs looked bad and he replaced them. He also found what looked like arcing on the coils and replaced all of the coils. I then rode it and the bike definitely ran better but the on off is still there.

Well, I was watching a video and this guy started to describe nearly the exact same problem I am having. If you would, please watch this attached video and start watching at 11:00 minutes in.

He described some sort of Yamaha programmed in fuel injector cutoff at, you guessed it, 4500 rpm. I think that when I am cruising around that I may be (unintentionally) engaging this injector cutoff over and over again. Not that I want this to happen but it always seems to be right at the rpm I like to ride it at. Take a listen and tell me what you think.

 
Then stop wasting everyone's time. We gave you answers and you just argue like a child. GO AWAY!
A little harsh my friend. I mean based on what Yamaha says, plugs should last 29,000 miles, I only have 6000. I would also think that at 6000 miles the coils shouldn't have gone. I would also think that through testing, Yamaha would have found out the bike had this same issue if it had to do with the programming of the ECU. I for one don't like just replacing parts for the heck of it hoping to see what sticks. That may be your cup of tea but I have a little more discretion.
 
This fired some neurons from a similar problem I had.
I second the coil check - I had two fail on my 2007 @ 36k mi, and replaced all four. I had spent an excessive amount of time trying to diagnose the issue (I'm not that bright), and finally just replaced them. Problem solved, for at least the ensuing 36k.

I had to replace my ECU as well as the coils. I never had any of these issues with my VFR with gear driven cams lol. Then again, this bike has more power?
 
Thanks for the response. So far the shop said the plugs looked bad, and they did, so they were replaced. The coils may have been the cause since they are 15 years old, I said go ahead and replace all of them since he didn’t charge me any labor on that.
We are now down to the ECU flash.
Even though it appears that the ECU flash may solve the problem, I didn’t want to go down that path first. To me all the other things don’t alter anything and they are problem solving arrows that are shot at the problem. Probably next month I’ll have Vcyclenut do the flash. I spoke to him and he is a really nice guy, and seemed very knowledgeable about it. I am betting from what he said, this is going to be it.
 
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