First you have to understand how a tuned pipe works. The tuned pipe is designed in a way to utilize the back pressure in a performance enhancing form (such as having the back pressure timed to force the piston down while in the down stroke motion). By drilling another hole in your pipe you have completely ruined this tuning effect.

Another thing that is probably the most major problem with your modification is that when you drill a second hole in the tuned pipe you reduce the pressure (since you are allowing more exhaust to escape), by doing this you are reducing the pressure to the fuel tank. Reduced pressure to the fuel tank forces less fuel into the engine. This is exactly the same thing as leaning out your engine which will cause it to run hotter and potentially damage it.

You can have the same effect on engine performance by leaning your mixture and you won't ruin the "tuning" effect of your pipe. I'm not saying that you should lean out your mixture (nor am I going to go into an entire engine setup discussion here), I'm just letting you know that you obtained a false increase in performance that will eventually damage your engine.

Everyone has to remember that the designers of these components spend a lot of money in designing them. They want you to go as fast as you can as well. Try listening to them and running their stuff as intended and you will go much faster and be more consistent.