I have used the old 36mm mikuni, the 33mm mikuni and the 35mm keihin. The 36mm was the cleanest install. I still had to do some grinding withthe 35mm and also put a spacer under the back of the gastank to clear the top of the carburetor. For a stock motor, I would go with the 33mm, it gives better low speed response in conjunction with a oversized headpipe, I would not use an aftermarket silencer unless I just had the money laying around.. The grinding is not that hard and does not affect the strength of the frame, I have done it on 2 of the KLX's I have owned with no problems.
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You weren't born knowing this stuff.