PK numbers

The 3.9M is just a 5.2M with two less cylinders. It again, has only 3 cylinders firing per revolution. But it has the same good heads that the 5.2 has. The same 3.91 bore, and the same 3.315 stroke. And AFAIK the same compression and cam specs.
So two otherwise identical trucks, one a 5.2M and the other a 3.9M. will instantly give you a fair comparison to show you exactly what the value is of those two missing cylinders. But the key here is "otherwise identical". You cannot compare a 3.91 geared 5.2 with a 2600stall TC, against a 3.9 with a 2200TC and 3.55s. Even tire diameters can,on a truck,make a huge difference.
Take your 5.2 and put the same rear gear and tires on it that are on your 3.9 equipped truck. Then disable two cylinders. Adjust the weights to match, stick your accelerometer on the windshield, and take her for a blast. Pound for pound, gear for gear, and stall for stall, the 5.2 less two cylinders should run pretty much the same as the 3.9.
But the Dakota/Durango has aero on their side; whereas the D100 is pug-nosed brick, that the faster you push it to go, it requires exponentially more power to push it thru the air. The math says everytime you double the speed, it takes double-double the power. So if the D-100 takes 35hp to go 40MPH, then theoretically it will take 140 to go 80, and 560 to go 160.
But maybe the Dakota only takes 25hp, because of the aero, to go 40, then 100 to go 80 and just 400 to go 160.
Now if you force the Dakota to run 3.21s with 28" tires, like the D-100 has, then in direct gear at 60mph, the rpm is 2310 @zero slip. So you got no accelerating capability left; the trans has to kick down into second. The Rs will rise to 3920 plus say 15/20% TC slip, so maybe 4500 on the tach. The engine is well beyond the torque peak, right on the power peak, getting set to slide down the back side. So really, you would get a lot of roaring, but not a lot of RapidTransit. And of course the stall is way back there at maybe 2200, so no help at all.
I know you really like the D-100,( I like my homely-D too) but if the 3.21s have to stay, then I would load it up and go for a test run, to see at what roadspeed, and under what conditions, the power really sucks. And I would do it with my accelerometer glued to the windshield, to remove my butt-dyno from the equation. My G-tek-Pro will also generate a horsepower curve and so I can very quickly analyze where in the roadspeed range, the power is tanking, and from those two, I can formulate a plan of attack. I got mine 20 years ago, when they were still cheap. But I gotta tell ya, whatever you gotta pay it's the best money you will ever spend, on account of you can spend your HotRod money on the most bang for the buck, where it will do the most good..
And I gotta remind you, that there are many things you can do to your slanty to make more power; but more power always comes at a higher rpm. And if the 3.21s gotta stay, then you will have a hard time to get to that higher rpm, in every gear except first, and you will never get to it in third gear.
For instance, with a power peak at 4800, with 3.21s and 28s, you will get there
in first gear at ~38 mph,
in second at ~72, and
in third at ~113.
So while you can build your slanty up in power, if that power is in a place you cannot get to, or where it does no good, then you are kindof pooched.
So shifting into Second at say 5100, the Rpm will drop to 3000, and now your engine has to labor up the powercurve again, beginning at 38mph. Of course it will be sucked out for a long time.......
Now say you had 3.91s,
then first gear would be revved out by 34mph, and by 38mph in second, the Rs will already have climbed to maybe 3200, so yur 200 rpm higher up the curve.
But, if the engine you built, sacrifices 20hp at 3200 rpm to get 30hp at 4800........... then the break even point in second gear might not come, I'm just guessing here, until 60mph with the 3.21s. So great, you got more power at 72 mph, but less from 38 to 60.
The point is this; you gotta analyze the whole combo, and not get stuck on high-rpm power.
If you need power at 38 to 60, you gotta build the whole combo to put it there. and castrating your 225 with 3.21s is not gonna help it one bit. If the 3.21s absolutely have to stay, like you keep saying, then upcamming the slanty, for more power at the top, is, IMO, the wrong thing to do. You would be way ahead to just supercharge it. That is the best way, IMO, for the 225 to get thru the 1-2 split of 1.45/2.45=.59
So once again, get yourself a G-tek or some type of accelerometer with graphing capabilities, and go generate some power curves. From those, you can figure out what to do next.