See my thread on two stroke theory and process model. It has a animation of a running engine at the botttom. If you changed the pipe, i am assuming that the new pipe is a fatty or similar. The larger expantion of the new pipe changes the return wave and you will have to increase jetting size to throw in more fuel, other wise the overlap of the stroke goes to zero or less and the combustion stroke ends up trying to burn already combusted fuel/air.