THE PLT REPORTED HE HAD A PROBLEM WITH THE SPARK PLUGS LOADING UP BEFORE HE DEPARTED SACRAMENTO, CA ON A X-COUNTRY & THER MAGNETO (MAG) HAD BEEN OVERHAULED BEFORE HE DEPARTED. HE STATED THE ENG RAN WELL 'EXCEPT FOR BRIEF PLUG LOAD (ONE CYL)CLEARED BY LEANING MIXTURE.' EN ROUTE STOPS WERE MADE AT TEHACHAPI, CA & FLAGSTAFF, AZ FOR FUEL. THE PLT SAID THAT DURING TAKEOFF AT FLAGSTAFF, THE ENG LOST POWER AT APRX 100 FT AGL. HOWEVER, WITNESSES REPORTED THE ENG WAS MISSING ON THE TAKEOFF ROLL. ONE WITNESS, A CFI, STATED THAT FROM WHERE HE 1ST HEARD THE ENG, IT WAS MISSING STEADILY, BUT THE ACFTCONTINUED ON THE TAKEOFF & ROLLED APRX ANOTHER 1500 FT BEFORE THE PLT TOOK OFF WITH THE ENG STILL MISSING. AFTER TAKING OFF, THE ACFT SETTLED, HIT TREETOPS & CRASHED. THE R MAG WAS FOUND AT 3 DEG BEFORE-TOP-DEAD-CENTER (BTDC). HOWEVER, THERE WERE SCRAPE MARKS WHERE IT HAD ROTATED; THE RETAINING NUTS WERE SNUG, BUT NO TIGHT. ALSO, THE LEFT MAG WAS IN ITS PROPER POSITION TO FIRE AT 25 DEG BTDC. THE ARPT ELEVATION WAS 7012 FT.