So history first is I did my valve clearance at 17k miles and they were perfect, always use mobile1 10w40 oil, K&N oil filter, stock air filter, JTI S2 exhaust and power commander 3.

I am currently at 22k miles and I had a slight knock that I thought was just a simple valve adjustment that started about 200 miles ago. As I kept riding it would slightly get louder as I ride more. Power was all still there and nothing changed.

So yesterday I took the day off and did the whole valve clearance routine and everything still was perfectly in spec and had it back together in about 4 hours. While it was apart I cleaned the fuel pump filter and tightened my throttle cables slightly. As I got back on the bike the knock was still there and now it will hit an imaginary rev limiter once I pass 3k RPM. The clutch is just let all the way out at like 2800 RPM. It never did this before. I also never touched the clutch so I don't think it's that.

I tried giving it some gas but even 3/4 throttle the bike won't go any faster or pass 3500 RPM max!

Could I have a 2 connections messed up? There are 2 that are exactly the same. The spark plugs are pretty good and throttle bodies all open as they should. There was a small red wire that is that goes into a connector along with 5 other wires that got unplugged from its socket if that makes sense, and I put it back in its place. Also tested the air box flapper with my hand by pushing it up and down.

I have new gas and no FI light on other than the EGCV Valve light that has been there for more than 12k miles. It will idle perfectly and still warms up at 1800 RPM and goes down to 1100 RPM like normal. Air or gas is my guess or wrong connections?

Any ideas?