Chase:

The info I have states that the bulwarks were 8" oak. The engines were protected by lowering them into the hold, i.e. below the water line. If there was additional protection, I've never heard of it.

As regards the battery, a letter from Acting Ensign Symmes Browne, published in Letters From the Freshwater Navy, states that a 32-pounder was mounted in the ship's Wardroom, which was located aft of the wheelhouses. This info is partially confirmed by Lt-Cdr William Gwin's report of the Tyler's fight with the CSS Arkansas, in which Gwin reports that "we could bring but one gun to bear on our pursuer."

You are correct about the smaller pieces (howitzers) being mounted on the spar deck, which would mean that pretty much the only space available for the 30-pounders would have been at the bow ports. The NHC collection contains a photo (http://www.history.navy.mil/photos/images/h49000/h49976.jpg) that clearly shows a muzzle that looks too small to be an 8" sticking out of the port-side bow port.