It sounds like something is wrong with the shoot thru hull transducer; either in the transducer itself or in its mounting. It will need to be removed, tested and possibly replaced. You can test it be removing any remaining epoxy and holding it over the side of the boat in the water, while drifting, and see if you get a good depth reading or not.
This new problem that you have; what transducer is plugged up to it when that happens?