Agreed. You're talking about building an engine that was originally designed as a gas engine, was already "stretched" into a mildly powerful but reliable diesel engine, and was stretched again to get the multi-fuel ability.
What kind of direct injection are you talking about? Hydraulic or common rail? Either way, I'm thinking you'd be looking at a set of cylinder heads, there's not a lot to work with. Then you've got to figure you need 30X or better camshaft revolution sensing to make it work at a minimum, probably a crankshaft sensor, neother of which have a provision to trigger a sensor. When you get that, you're moving on to a high pressure pump (fuel or oil) that has nowhere to go. You've got to get the pump, a regulator, a pressure sensor all wired in, and you have to plumb it somewhere... There are no passages in the head, nor was the head designed in such a way that you could have a "straight shot" to have passages made into them. Now you're out of the "slobbering" injectors anyhow, which is one of the key differences in the combustion process, but you've still got the "goofy" cup in the piston that's designed to burn liquid fuel off of the side. It won't have that any more, it'll be burning suspended atomized fuel, for which the pistion shape is just not a good one. Incidentally, therein lies the biggest problem with turning up a julti-fuel to modern standards. The fuel burns from a liquid form, not atomized. Thus the process heats the piston disproportionately, and the timing of the peak pressure becomes environmentally variable and too far removed from the mechanically timed injection event (either mechanically timed by a mechanical injector, or mechanically timed by a sensor sensing mechanical timing and passing that information along to the ECU), thus the control is very imprecise. Injection timing means squat. Timing of the peak pressure in the cylinder is what you're after to make downward force on the piston, and therefore horsepower. So now you're into that can of worms where the lower end is needing modifications anyhow.
And the electronics... Speaking of cans of worms... Robbing the electronics is not difficult, even if you had to build your own harnesses. (I said not difficult, I did NOT say not time consuming... The only thing that makes it difficult is if you try to take shortcuts). You do run into a problem though. You've now got a system that does NOT have the same characteristics as the donor, so you can't set it up and get it running right based on the silver bullet method. You've got to have a scanner that can communicate with it. And that does not mean a code reader from the Auto Zoo... Aftermarket scanners can read most of what's availavle, but they're VERY, VERY limited. They break down the silver bullet theory, but again, that's already out the window. You really need a dealer level of software to set this up. (You'll be surprised, it's not as much as you think... That's only a small issue...). Next, you need the module to be willing to "wake up" and go too work. That's going to mean that you need a lot of other modules on the network... You are going to find that you need modules to do things that the truck is not equipped with. Now you're into custom code... You can grab a "standardized" off the shelf product for some engines, not so much so for others. But it's still written with something in mind, and now your project is limited by that fact..
This list just goes on and on and on and on.... Really, an electronic diesel is a whole different animal unto it's self. They share the same concept of a crankshaft and pistons going up and down, but so does a gas engine, a weed wacker engine, your air compressor.... You're essentially starting from scratch.
My thoughts, if you absolutely need horsepower...
A more modern engine. The 6BT comes to mind, but there's lots of good ones to choose from.
Seek out the parts, and build the multi back into a straight diesel. It was used in marine and agricultural applications in that form, the parts are there, and from that point you can be a lot more comfortable with the "standard" modifications for a mechanical diesel engine, because at that point it IS a diesel engine, instead of what it is now, a "heavily modified and strangely tuned" diesel engine, that really, really looks like a diesel engine from the outside and makes you wonder why you can't get the torque and horsepower that you'd expect to be able to get with a modern diesel engine. It was pretty powerful in it's day. Remember that over the road truck tractors were carrying full loads with gasoline powered engines rated at about a hundred and fifty horsepower. You had to shift them a lot, but you could still find people willing to learn a skill and shift them well. It's just how stuff was built in that time. It had what it had, and could deliver it all day, every day. Today's philosiphy is different. You can get stupid horsepower out of less engine, but intermittant use only because the engine can't take it. So when you pull out and pass, you don't have to be troubled and inconvenienced by noticing your automatic transmission backshifting it's self while you do absolutely nothing but smash the stupid pedal down. (OK, starting on a tangent/rant, I'm done...)
Personally, I don't think the rest of the truck was built for the horsepower available in modern standards either. "Back in the day" these trucks were well powered when compared to regular commercial stuff, but there was a difference. Over the road drivers had a couple of transmissions and enough gear combinations to where they could spend twenty minutes and never grind the same gear twice. Smaller in town delivery trucks has less gears, but many of them were still unsynchronized. The Deuce wasn't exactly a marvel at that time, but it was nice. Anyhow, if I needed more then I think I'd be less inclined to go after the engine, and leave it like it is, so you can stay right after it for as long as you like. I think I'd be more inclined to go after the transmission and/or transfer case, and get enough useable gears that the engine speed and road speed could be matched, so that horsepower the engine is capable of can actually make it to the road.