You didn't flood the motor, you hydro-locked it. Liquid/Water is not compressible, take a engine that is used to compressing air (easily done), and spinning at say...3,000rpm, and pour water in it. Cylinders with water will be forced to try and compress it by the combustion in the other cylinders...since it won't compress, things break.
You probably have "rod-knock" (bent rod, or two or three) and it will condemn your engine as bad/broken/dying/no good. Start lookin for another..