I believe that the prototype aircraft had the u/c selector positioned on the left hand side just forward of the throttles, this could possibly result in an inadvertant "down" selection if the throttle was pushed fully forward, I remember being told that one aircraft had a down selection at mach 2 resulting in an airframe loss, the u/c selector was moved to prevent a reoccurence.
Early prototypes had canopy losses in flight, this was cured by modifying the mechanism cams.
One Mk 53 belly landed at Tabuk and the gun pack and ventral tank absorbed the impact, the aircraft did not sustain any serious damage and was repairable.
The Lightning was designed and built in very austere conditions with very little political commitment, it really was a classic aircraft.
Best regards,
om15