You can get a R&D filter here:
YAMAHA FX HO / FX140 They are better and cheaper than the OEM. You can actually run this engine without a filter to see if you get any improvement. If no improvement without the filter, I'd do a compression check next......should be 185-200+ with the engine warm and the throttle held wide open during the check. If the compression is good on all cylinders, you most likely have dirty fuel injectors.......I'd pull them and have them professionally cleaned.