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There is only a 236lb weight difference between the D4 and the D6. The engines are both the same size but the D6 is about 10 inches longer. These boats usually have a 14 degree deadrise so they don't need a ton of HP. However 300hp isn't enough for a boat that will probably weigh around 10,000lbs.
This biggest concern I would have is not the single engine, but the duoprop drive. I have heard they don't hold up well with diesel power - hell they need to be rebuilt every 500-700 hrs or so with 425 hp gassers, which have less torque than the D6's. I would probably opt for the simplicity of the outboards. If a single inboard diesel where a choice, I'd probably go with that.
GO DIESEL ...............
I moved 4 years ago from twin 200hp Mercs at a seasonal average of 9.9 gph w/ more service requirements & all the small PIA troubles to a trouble free diesel power plant averaging 3.2 gph for the same and more offshore fishing, trolling and cruising. I can't speak to the new common rail motors personally, but hear great things. My Cummins 370 6BTA has been stellar!
The post about slow-trolling raises a good point. You probably won't be able to troll less than 3 or 4 knots with a single i/o (gas or diesel). Twin outboards let you get down to 1 to 1.5 knots on one engine. Of course, this is a moot point if you don't slow troll.
As far as maintenance, an outboard is much easier to maintain yourself, in terms of access to the critical components. If the boat is on a trailer, you can service the engine while standing upright (no bending over or laying on your stomach). Very little knuckle-busting involved with outboards.
No winterizing of the engines is a huge deal to me (even in temperate NC). If I want to fish in February, I just drop the boat in the water. The only real winterizing I have to do is on my freshwater tank.
Consider the Yamaha F350 with built in electronic controls ( inside helm and cockpit helm). Also consider a more robust kicker than the 8hp Maybe a 20 to 40. Tie the 2 motors together with a good front mount tie bar. With a steering helm in the cockpit, and controls for the kicker at the cockpit helm, you will be set up nicely for Northwest fishing. A transom door is always handy to have.
Thousands of people fish out of boats with outboards, so don't be overly concerned with that issue.
Experienced boatmen who put very large amounts of hours on their boats will always prefer diesel. For the recreational boater, it becomes more of a numbers/convenience game. How many hours will the motor actually be running per year, cost of fuel, cost of motor, convenience of having one motor over another. The diesel smell issue only becomes apparent to me when running slowly, or trolling with the wind and the odor comes back over the transom.
Great additional feedback. I will try and respond to the questions you have posed. The D6 that would be installed would be a 370HP, but I was able to drive the same boat with a 350HP D6 in it, and it had plenty of power. It was very easy to get on step, and I never felt the need for more than about 1/2 throttle. While it is 370HP, it is also 650 foot-lbs of torque. I have looked for torque numbers on the Yamaha F350, and not been able to find them. I doubt that they are in this range, I would be concerned that this would be ample power. The two configurations that they currently offer this boat in is the D6 and twin 225's, and it is the same cost either way.
As for trolling speed with the D6, I would not use this motor to troll. There would be an 8HP kicker that can be run from the rear helm station for trolling with a built in 9 gallon gasoline tank. Bumping the power of this motor to a 15HP or so may be a good move if I am going to rely on it as my 'get home' motor as well.
I recently downsized from inboard Tiara to outboard pursuit...What i miss is the ability to upsize alternators for heavy loads and inverter...ability to heat hot water with the engine and a host of other things...I am against outdrives if one keeps the boat in the water ...for obvious reasons...why would any sane person cut a huge hole in the transom of the boat...this area is a notorious failure point......You should be able to do the math pretty easily for your break even point on cost...
If the prices were comparable I'd pick the diesel hands down. This is coming from the guy who generallyspits out a bunch of numbers as to why getting a diesel pickup truck generally doens't make any sense financially except for a small few.
As far as single vs twins, yes redundancy is nice but keep this in mind:
1)Not as redundant as you think. A massive electrical problem or a fuel problem can often kill two engines just as easily as one.
2)Two engines- twice the maintenance and twice the likelihood of somthing going wrong.
3)A pull start kicker with a dedicated fuel supply might make more sense.
4)In many cases, if you can't plane, youwill beat the bag out of the other motor, so you'll probably limp home at kicker speeds or call sea tow anyway
5)Yes, twins add a certain safety factor, but to say that you would never go out of sight of land with a single means you have to ease off the Kool Ade. Out of all the times I have been Stellwagen Bank (about 25 miles from any land) I have never done it in a twin engined boat.
6) Ever heard of single engine prop planes? Do you think any of them refuse to leave the ground without twins?
Another Vote for the diesels. I just sold a twin diesel boat and got another twin engine outboard (long story) but i havent even started fishing yet this year and already i cringe at the thought of fuel this year. Red diesel is CHEAP compared to unleaded.. AND SAFER!!
And to have dual station control you dont have to have electronic controls. There are other options for that. At a third of the price of electronic.
Re: Diesel vs. Twin Gas Outboards 
