From what I have seen they are very similar, but not identical. The cylinder, power valve, piston, rod, crank and carb all have different part numbers. The cases, transmission, clutch (not sure about the basket) and ignition are the same. Sometimes Yamaha will have a different part number, but the aftermarket doesn't. I believe Wiseco sells the same piston for both. Also stuff like the frames have different part numbers, but I don't believe there are any great geometry differences between the two and of course all the plastic is the same.
The front brake is full floating and I believe the disk is bigger, as previously stated, on the 01, but I have not ridden one to compare to my 2000.
Has anyone jetted their 2000 with 2001 specs?