Just to clarify the part number situation, the first three numbers/letters represent the vehicle model code, the following 5 numbers represent the actual part, the next two numbers the design code, and the last two the colour/finish code.
In essence, if the actual part element of the number is the same, the part is the same regardless of the model code placed before it. However a different design code will mean that the part has been modified, but will still fit retrospectively, even though it may not be the recommended design code for an older model. No prize for guessing that a different colour/finish code means the part has a different colour/finish, commonly used in bodywork part numbers.
You've said your bike is a 2009 model, this means that you require the filter with design code 02, as design code 00 is specified for 04-06 models, and design code 02 for 07-onwards models, not too sure what happened to 01 this time? Maybe they lost count...
Hope this helps,
Yamahaboyz