Solved - rough running on 05 Gen 1 1000

[PaulSmith]

The filter itself should probably be replaced every second or third service unless you have already upgraded to a K&N style cleanable filter. The point I was trying to make though was not about the filter itself but about the entrance to the airbox. if you have waterproofs, spare gloves or anything else under the seat that can partially block the airbox intake, it could cause the hesitation you have described.