Actually, you don't have the worst flowing heads. The D3's are usually fine and can be ported to near ridiculous numbers if you want to do that. The C8/C9 D0VE heads do have larger intake ports and no thermactor humps in the exhaust ports (Some D3's don't have those either), but they also have smaller combustion chamber volume which will bump up compression ratio without changing pistons, another plus, unless you are changing pistons anyway.
Honestly, I've seen some pretty powerful 460's running not so modified D3 heads, and I agree you're gonna get more bang for the buck doing what Ralph and GT said. First thing is to get the RPMS up to the 5000-5200 range to get the pump operating in it's optimal range (Sounds to me like the pump is fine, loading the engine up quite effectively) and that dinky carb is likely the biggest culprit that is mostly killing you. Go with an 800 at least or an 850 better yet. Hell a 750 would help a lot, but that's really too small!
Your intake is really the best dual plane available for the 460, so you're good there. The RV cam isn't so bad, but it's designed to throw the torque curve into the lower ranges rather than higher which would be optimal for a Jet Boat. Still probably better off than the standard truck grind.
Gotta be kinda careful just throwing cams at these things. I've seen and heard great results with the Comp 286, 292 and 305's, but the rest of the valvetrain has to be up to snuff, and geometry carefully checked when doing it. By that I mean screw in rocker studs (If the heads are not already equipped), guide plates, GOOD chromemoly pushrods, valvesprings and retainers rated for the particular cam/lifter set up you plan to run, etc. Valve spring seats may need to be machined to accommodate whatever valve springs are required as well.
Personally, we're in the season now! I'd leave it mostly alone, save for the carb, Place Diverter and ignition recommendations thus far for the time being. Be plenty of time over the winter to tear into the engine for more HP/speed if need be for next year. You've a better idea what is really going on by then also. Run it and have fun!
The D9 blocks, Ralph is correct. Really just a change from internal balance to eternal allowing smaller throw weights on the crankshaft. This also means the bores go further down into the block, which I don't know that there's a plus or minus either way. Just don't mix up the crankshafts with older cranks. I've not heard of any cylinder wall thickness differences or anything, just an issue with certain stroker setups not working with the '79 and later blocks.
Ray