The gasgas comes with an oversized front brake rotor. I think the main problem is that the front brake lines in 2001 were not steel braid and the front line is really "spongey". They went to steel braid lines in later years. He hasn't advertised them, but Les @ LT-Racing has a bunch of steel braid front brake lines for the gasgas in stock - these are very reasonably priced.
I would check the pads; I like the compound on stock nissin pads, in tight woods they are a good compromise between providing brake feel and stopping power. But if you want greater stopping power - you can go with a compound with a greater coefficient of friction.
When was the last time you flushed out the brake fluid? I usually use motul RBF600 brake fluid for a higher boiling point - but any good dot 4 works well. (FYI - silicone based dot5 is not compatible with dot3/4).
jeff