On May 8, 1999, at 0750 hours mountain standard time, an amateur built experimental Matter Glasair-SH-2R, N6DM, collided with a fence during a landing overrun on runway 3 at the St. Johns, Arizona, airport. The aircraft sustained substantial damage. The aircraft was owned and operated by the pilot under 14 CFR Part 91 when the accident occurred. The private pilot and passenger sustained minor injuries. The pilot did not file a flight plan for the personal cross-country flight. The flight originated at Payson, Arizona, at 0700, and was destined for Pampa, Texas. Visual meteorological conditions prevailed at the time of the accident. The pilot stated he was about 35 to 40 minutes into the flight at 12,000 feet in cruise flight when he smelled a smoke odor from the cockpit area, and began to see smoke coming from a microswitch for the flap motor. He stated that he elected to pull the flap motor circuit breaker when he noticed that the flap motor area under the passenger's seat was hot to the touch. He then turned off all electrical power. He said his passenger became excited and he elected to land at St. Johns to investigate the problem. He turned the power back on the airplane to extend the gear and make an announcement with his landing intentions, and to get runway information. He said he was told that the winds were "calm." He stated in the pilot/operator report that he set up an emergency descent from 11,500 feet direct to St. Johns airport, with all power to the engine and airplane turned off, and subsequently misjudged the approach to runway 3. He then turned power back on and restarted the engine and gained altitude for an approach to runway 32. After he determined landing was assured, he turned off the fuel and landed on runway 32. During the landing attempt he subsequently overshot the touchdown point, overran the runway, and collided with an airport boundary fence. The pilot estimated that he ran off the runway going about 30 mph, and that the airplane fell about 6 to 10 feet vertically down an embankment landing on the nose gear. The Federal Aviation Administration (FAA) Airworthiness Inspector who examined the aircraft at the request of the Safety Board said that two wire splices, which were connected to the flap motor, were touching each other and had caused the smoke. The wire splice area was charred and discolored from the heat. The inspector determined that there was no fire damage to the airplane. Additionally, the three-position flap motor switch was examined. In the down position the switch is spring loaded to return to neutral once finger pressure is removed. In the flaps up position, the switch must be physically returned to the neutral position. There are no limit stop proximity switches in the system and the motor will continue to run in either the up or down directions if the cockpit switch is in other than the neutral position. The FAA inspector determined that the heat came from the flap motor continuing to run after the pilot retracted the flaps after takeoff, but did not reposition the switch to the neutral position.