They made a huge amount of changes between those years. The 2003 model has a lot of changes over the 99. The 03 has the high output motor which consists of a better camshaft and bigger 40 mm carb. Here is a list of all other things I can remember that they had changed.
Longer travel front struts and rear shocks
Braided steel brake lines
Primary clutch - with engine braking
Secondary clutch - with engine braking
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