The best suggestion I can make is: come up with a plan first... Then stick to the plan throughout the build, if you're gonna do it in chunks. Do not start off building one shortblock for a particular combo, then change directions and go with different heads or intake or whatever. More times than not, you're gonna end up with a miss-matched pile that doesn't perform as you want it to or it can/should. If you plan and start buying parts for a particular build, stick to the plan.
Second... Which actually should be the first thing... In order to come up with a plan... Gonna need to Figure out exactly what your goal and expectations of what you want to build and what you have to work with. 650hp iron head 496 is gonna be a different build than a 800hp 496... And different being pump gas vs race gas... Etc... Etc... Figure out what your goal with the boat is, and what sort of hp is gonna get you there... And what aspects are most inportant... And if you're not sure... Ask... No such thing as dumb questions... Just dumb shit people do for NOT asking questions.
And last... Figure a realistic budget... Obviously, since you're not going to build it all in one shot, you can stagger the costs over different phases... But ultimately, overall cost will have an effect on just what you can and cannot build... And how quickly you can build it. Not minding if it takes an entire season makes a larger sum rasier to swallow, but you have to weigh time vs cost... Want it sooner, but can't afford as much? Or want full bitchen, and can wait a little? Time and cost plays a pretty significant role in a build if you eant to get the best bang for your buck.
I started with this outline when I built stuff for myself as I like to buy parts once, and build something once and right the first time... and then continued it when I started building for customers... And thus far, I like to think it has worked pretty well and ended up with people being happy with what they got for their budget and needs.
I can tell you now though, built right (which includes machine work... Which often gets overlooked in how to build a boat engine to run and last), no matter what combo... A 496 should make a noticeable power, and especially torque, difference than the same build 454.
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