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Back off the two bolts installed, just loose enough to be able to rock the converter back and forth. Then turn the engine by hand to the third bolt spot. Alignment will go smoothly then. Don't forget to retighten the other two bolts to specs. This is a normal situation for almost all 350 and 400 torque converters.
To answer the last question . . . DO NOT run it with two bolts.
You would be well advised to run a thread cleaner or tap through the holes before trying again. Sounds to me like you had one crossthreaded and this condition will not correct itself.