Geez, this isn't the sort of thing I should try to tackle at 4 A.M., but here goes...
Trucks, and diesels especially, are not my area of expertise. I can, however, tell you plenty about engine configurations.
The Inline 6 is a terrific engine design. Despite the fact that auto manufacturers prefer the V6's smaller size, it's not really that much bigger and is intrinsically superior. The reason the I6 is so great is that it's completely balanced by nature. Vertical and transverse vibrations are cancelled out completely. This eliminates the need for a balancer. Compare that to a big truck V6. Since it's a big motor, I'll assume it's a 90 degree (possibly a scaled-down V8 even). It's going to need a balancer. There goes some of your power and efficiency right there. Now let's look at the valvetrain. The V6 has twice as much of just about everything because it's split into two banks. Frictional losses from the extra camshaft outweigh the V6's only component advantage, 4 main bearings versus the I6's 7.
That's it in a nutshell, without resorting to complicated math (which I don't particularly like). The only real reason to go for a V6 is its smaller size. When packaging isn't an issue, you'll see the I6 used much more often. That's why when Rolls-Royce and Bugatti didn't want to put a V12 in a certain car, they turned to the I6. And you probably should too.
As for your boat, get the rotary engines. They'll serve you well, and with less demanding work than they would get in a car, they'll last forever. I won't get into why they're so nice, not in this post anyway.