I'd say that I would figure out 1)What you're trying to do with this thing (goals)... Pump gas friendly big inch deal? Or high compression big hp deal? Cruiser? River hot rod? Full track and occasional river? Etc... 2) What do you actually have that you intend on using and/or to work with? and last... 3) What sort of final budget and time frame of build do you have in mind (small budget and need it done next week? Or build over time and aquire parts as you can afford them?)
If you can figure those three things out... then you can go about how you're gonna go about your build to meet those requirements and not either end up with something you compromise and are not happy with, or money spent on the wrong things, or a hodgepodge of parts that don't seem to work well together.
As far as generalities... the 540-555 combination is about your best bang for your buck as far as starting build from scratch goes. Pump gas deals in that range can easily make 800+hp with a nice set of done up nice heads and a camshaft that is ground for the combination and not just the 2nd from the biggest in the catalog. Obviously, higher compression (race fuel) builds can vary depending on just how stout you wish to go... from a reliable, river driver 13-ish:1 deal 950+hp to a full tilt drag, high matinance deal that would be well over 1K hp. The main difference in any of the builds is really, your goals, how often you want to work on the thing, and how deep into your pocket you wish to reach.
Several areas I would say that money is well spent is on quality parts and good machine work. Both of those can make the difference between something that rips and runs for years, and something that shits the bed the first time out. Another thing to keep in mind if you're swapmeet/craigslist/ebay bound for something like cylinder heads... unless you know where the parts have been, and who has done work on them... you must assume that they will need everything done. More times than not, I have found people bring in heads that are "fresh" or "only one season on them" that they bought for a "smoking deal" have one or more combination of the following: blown out guides, bullshit valve job, butcher port work, mismatched chamber sizes, corrosion, cracks, and/or used up valvetrain parts. When I did up Lupo's heads... even though they were supposed to be fairly new... the guides were shot due to poor valvetrain geometry, the chambers between heads were 4cc's different.
Build your bottom end with the best parts you can afford, and make sure ALL clearances are within a tolerance that is applicable to not only a marine engine, but your intended use.
Heads, intake, and cam is where the power is at... select wisely and make sure it all jives together. Poorly matched parts cost power and can have an adverse effect on reliability.
Check everything till you can recall what each part measures and it's clearances are off the top of your head (but still be sure to write everything down)... you can never check you work too much while mocking up and assembling... often times, if a mistake anywhere down the line has been made, THIS is where it will be caught and hopefully corrected before it goes in the boat. Assembling/building an engine is more than just stuffing the parts together and assembling a jigsaw puzzle... you need to check clearances, fit, valvetrain geometry, etc...
These are a few things to think about before you dive in... Hope this helps.
The Bostick ®