Re: submerged up to the plugs
Yes, or leave the plugs in temporarily until it is full and then flush. For example, the transmission has a vent up in the shift tower that I'm sure the water entered into the trans case. Short of pulling the shift tower off, the most you will be able to fill it is to the upper filler plug. The same with the engine as I am sure it entered around the distributer housing and filled the crankcase up to that level. You may even want to remove the valve chamber cover just to flush that area too.
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