the captain's failure to follow standard operating procedure for landing on a contaminated ruway in that he touched down long, which combined with his delayed braking resulted in a runway overrun. Contributing factors were the captain's failure to maintain runway alignment following his disconnect of the autopilot, the gusty crosswind and the wet runway. In addition, the following were contributing factors: (1) the airport operator's failure to fill in a ditch in the runway safety area, (2) the FAA's granting of 14 CFR Part 139 approval to the airport when the runway safety area (RSA) did not meet the recommended length for a Part 139 airport, and (3) the FAA's continued lack of acknowledgement to the airport of the inadequate RSA following their annual airport inspection checks.