Duranh can you please explain this to me. I am on the fence with my bike. I was looking at the Screamin Eagle Pro 110 Performance Up grade Kit with a V&H Pro Pipe. Of course the HD shop says to do it. But I do not know the REAL pros and cons. I am planning to call another shop to see what they say. Any input would be great! Hope I am not hijacking this thread 
It probably is a hijack of the thread but since he has already answered his own question I suppose it is OK.
There are others on this forum with far deeper knowledge and better abilities when it comes to sharing that knowledge but I will give it a try.
The stock cams do not open the valves fast enough, far enough or keep them open long enough for the motor to run like it could. One of the ways that HD is able to get these bikes to pass the EPA tests is to greatly reduce this valve overlap, or if you bought your bike in Cali, eliminate the overlap altogether. This keeps the raw fuel from escaping through the exhaust and reduces emissions so they pass the test. Another thing that they do is run the fuel as lean as possible so that all of the fuel that goes into the cylinder is used up and none or very little makes it out of the tail pipe.
My personal opinion is that going to a High Flow intake, exhaust and adding a tuner is a step in the right direction and will solve the lean air/fuel mixture issues it is not money well spent unless you add the right cam to the mix as well.
It is possible to actually get more air/fuel in to the cylinder than the volume of space would normally allow. Having a slight overlap in your valve timing is what makes this to happen. As the spent hot air is going out of your cylinder through the exhaust it creates a bit of a vacuum, so while the air is rushing out of the cylinder it actually pulls the new fresh air in, allowing you to get more that 100% efficiency. More A/F you have in the cylinder when the plug ignites the bigger the explosion, the greater the power. This is scavenging in a nut shell.
One more thing that helps with this is a good tuned exhaust, Pro-Pipe is a great choice and I have run several in the past on different bikes. Just think of it this way, allowing more air into and out of your motor will help, but allowing more air
through your motor will help much more.
This is a much simpler quote from some auto site.
The operation of intake and exhaust valves overlaps nearing the end of the exhaust stroke because the intake valve actually starts to open before the piston has completed its travel to the top of the cylinder. The overlap is supposed to take advantage of the scavenging effect whereby the sudden rush of air-fuel mixture suddenly entering the combustion chamber forces more of the exhaust gases out of it. Overlapping the intake and exhaust strokes also makes engine run more smoothly.