Have you removed the fuel tap at all? Start with that and flush the tank with water, could be plenty of dirt sticking at the bottom. Just give it a good clean and when you put it back together make sure there isn't any water left at all, that could lead to serious problems. Also check your air-filter, if its slightly oily that is normal. Check the seal is still intact between your filter and airbox outlet, I imagine if there isn't it can let dust and dirt get through which will eventually cause issues.
And as the others said, an in-line fuel filter is almost a must-have. You can buy them in a bundle for next to nothing.