If anyone is interested.
Exhaust pulses are used to keep the fresh intake charge in the cylinder during the valve overlap (both intake and exhaust valves open at the same time). The reflected wave acts as a damn at the exhaust port and would be tuned to arrive in the mid to low rev, dependent on what your looking for and there are equations to work it out. In brief its longer header for lower RPM, shorter for higher RPM. Higher RPM offers less time for it to happen so is simply of less use if any there. It occurs when there is a change in pipe diameter or a sharp turn. It will never enter the cylinder itself and stop fuel air getting in simply because the port reflects it back. How much use it is depends on many other aspects of the engine tune. Decat headers for example often show an increase in the low-mid range power because of the different and smaller Y joint so a stronger pulse is sent back up. It also obviously offers less restriction in flow with no cat in line so pumping losses are reduced at high RPM.
Intake length is partly about keeping the fuel in the inlet track. If you look at an engine with bellmouths (the intake pipes are simple bellmouths that exit in the airbox) on and look in while giving the throttle a good twist you will see a mist of fuel making its way out. Too short a track and the fuel can escape. As ever it isn't so simple though because there are pulsed involved here as well so a long intake track that will keep the fuel in at all times wont be the best for a high revving engine. Similar to the exhaust tuning longer is best for low-mid and short for high RPM.
Aftermarket exhaust manufacturers exist because they are in part free from what a mass production design has to cope with. They can play to a point with the tuned length and general packaging to suit what a purchaser wants I.E race bike or slow plodder. Whether its better or worse for a particular person is dependent on them. They also dont have so many regulations to cope with such as they can sell an exhaust without a CAT where the main manufacturer cant.
Both intake and exhaust tuning really do only offer small gains, even when tuned properly but they are noticeable to the butt dyno and a real dyno. As I said earlier though if not tuned properly they can make losses which is the opposite from what your actually trying to achieve. To get the best use from an exhaust and air filter change either a ECU fuel remap is required or something like a power commander fitted. There is a thread over on UKGsers with a company offering ECU remaps. There are dyno graphs posted that show even on a stock bike there are benefits to a remap showing useful gains never mind after component changes.