Here's some info taken from
www.nitrorc.com:
"The construction of the tuned pipe works with the pressure pulses coming out of the exhaust port. The pulses resonate inside of the pipe and travel back into the manifold. The pressure pulse actually pushes the air/fuel mixture that escaped out the manifold back into the combustion chamber. This super-charges the combustion chamber and gives the 2-stroke engine its characteristic peak HP. This is the point in which the engine turns ON. You will know that you hit this point because the car will accelerate rapidly when the engine gets on the pipe. You can actually fine-tune when the engine will have this extra burst of power. The speed at which the pressure waves from the pipe synchronizes with the piston, is a function of the length from the belly of the tuned pipe (widest part) to the center of the glow plug. The longer the distance, the faster the engine will come on the pipe. If you want to delay the time when the engine hits the supercharge, then shorten the header and/or pipe. When you replace the stock header/manifold, keep in mind that there is a reason for a pipe's size and geometry. You can use this information to your advantage to strengthen your engine's power band. A bad decision in the exhaust department can actually lower engine performance. "
Personally, if you find that you need to shorten the distance of your exhaust I would only cut the header. This is becuase the shape of the pipe is part of it's tuning. Change the shape and you'll change it's tuning characteristics.