I just got a new Zodiac Pro 12 with a 60Hp Mercury 4 stroke. Last Saturday on Lake Michigan myself and one other diver were starting to head back to the harbor in 5-6ft seas. We quickly found that we had water literally pouring in the back of the boat at low speeds (the battery box was totally underwater). I'm assuming this isn't normal

and am looking for some advice.
I picked up an automatic bilge pump today to install but what can I do to keep most of the water in the lake on the outside of the boat? I noticed that the boat shop installed the motor mount about 1.5 inches up off the top of the transom, they said it was so the anti-cavitation plate would be even with the keel of the boat. They are suggesting lowering the engine..
I haven't read anything like this here yet so I thought I'd tap into your collective wisdom...
Bob