There is certainly no great revelation that it is harder to get FF cameras working with wide rectilinears, behind dome ports, than DX cameras. The trouble about being one of the first with a system is that you are the guinea pig, Matt. The rest of us learn from you. At least here in Wetpixel it is easier to get in contact with others in the same boat.
I was always able to get good corner sharpness out of the 17-35mm on film (although ignore the housing manufacturer's recommendation). You could try a shorter port extension ring and stronger dioptre. The 14mm is much more troublesome to set up well.
At least your camera works. I got an email today about a guy who took 2 D3s to Lembeh and both stopped working because of flash-card issues (maybe related to strobe issues - which was something I discovered the D2X suffered with in the early days).
Alex
To follow Scott's point, I actually see the D3 as an inferior UW camera to the D300. Its bigger, heavier (on land) and has less spread of AF sensors. D3 has a better viewfinder. But it can't use a 10-17mm FE zoom (properly), and has problems with wide rectilinears. For macro the 12MP of the D300 give you more depth of field for a given subject size in the frame. At low ISO people argue the D300 has slightly better IQ, although its marginal. D300 has better AF spread in frame for off centre compositions. D3 amazing at high ISO - which is good for available light wrecks, so worth it if this is an important part of your photography.