Things that evolved throughout the years were porting, pipes, carbs, ignitions, pistons, etc... Those can make a big difference in how the motor runts, but the engine is the same basic design. I think you can swap cylinders between any of those years, but you might need to figure out what piston and head would work best if you are mixing cylinders and bottom ends.
Maybe get your '96 ported to '01 specs or put on '01 cylinder on the '96.
I'm surprised the '01 has a 14 tooth counter shaft. I know that rear sprockets can vary depending on year, but I thought they all had 13t on the front sprocket.