I want to start this by saying I love my bike a lot.

The problems I'm experiencing goes as follows, A slight ticking in the engine head that starts when the bike is warm it isn't the CCT I got a dealership to install a manual one about a week ago. There is also a slight knock while cold near the bottom of the engine. I think near the transmission. Some background about the bike just so you have the information, I'm running 5/40 Rotella full synthetic with oil stabilizer. The bike has been dropped but wasn't major, just cosmetic except for a hydro lock from it being on its side. I was able to fix the hydro lock and reused the plugs after cleaning them quite well. The one thing that could have come from that is I tried to start the bike while hydro locked about 7 times because I'm new to this whole thing and an idiot also the bike has full power like really good power is where it needs to be and it's QUICK I haven't done a valve check but the bike only has 7k on it so it isn't likely. I love this bike and don't want anything to happen to her but I'm currently a broke college student. Also just to make sure it's ok its a 2006 and I did an o2 sensor delete to install a new pipe and now it shoots flames at redline would like input about that I did use the o2 sensor delete plug so that's correct. (The slight knock started a few days after the new exhaust install. These are my problems please help me keep my baby kicking thanks guys. REMEMBER THE PERSON TO HELP ME FIX THESE ISSUES WILL ACTUALLY GET 20 DOLLARS PAYPAL.

 

Duuuude you don't need to pay anybody for help; this is why forums exist!

Your knocking sound could be:

- Valve clearance and/or valve, camshaft issue.
- Piston ring
- Crankshaft bearings
among other things...

If you add an aftermarket exhaust, you must also bring it more air (airbox mods) and change the injection map of the bike (super important!).
You can buy a Power Commander or Vortex...

 

I don't think it's the Piston rings or the crankshaft bit I think your spot on with the valves the bike has a constant 14.7 to 1 fuel ratio set for the exhaust so I think the exhaust and ratio is ok for now however a power commander is in the wishlist for now. I'm gonna buy a feeler gauge and check it out soon but until then I want to make a list of other things any idea on what might cause the tick.

 

I've had both noises you are scared about since new. I'll hit 89,000 miles tonight on my way home. Make sure its a issue before you go nuts.

That being said, the fact you locked the motor and tried to start it a bunch could mean some sort of starter/flywheel/connecting rod issue.
No, you don't. Airbox mods? Where do you get that from?
With a full system including headers yes you are getting to the point of needed some fuel adjustment. With a slip on you need to do literally nothing. I've had my slip on yosh for over 50,000 miles with no mods what so ever.

OP- how do you know the engine is running at exactly 14.7? You say the bike is set for the exhaust, how exactly did you do that without some sort of fuel trim modifier like a power commander?