yeah if the Y pipe had any issues then it would show up when you added water to it.
If you sponge out all the water in the bilge, start the motor on muffs, check for water, move on if still dry. Since the drive is pulled it's not possible to check for leaks at the transom properly.
With the drive on I would get in the boat and have someone back the boat into the water only submerging the transom, even if you have to leave the stern straps on. With the transom in the water I would look and feel around for water entering at the transom, by the sounds of the amount coming in, it wouldn't take long. If nothing then put the boat in a little at a time until you see water start showing up in the bilge then check to see if it's coming in aft or forward.