If your truck is fast enough, and you just need more grunt on the trail. Wouldn't an underdrive unit before a divorced transfer case do that for you? I agree with you about autos, altho I do not hate the c6 quite as much as others. Simply because it is, as mentioned, bullet proof. It really is. Personally, because they're everywhere around here, I will eventually be switching out to a ZF.
Now I haven't seen flow numbers on our intake manifolds. But simply looking at them, it must be abysmal. However even with a flowbench to test and build a full custom lowrise. At diesel RPMs you're really only looking at the cylinder getting like 5% more air. To get that high you'll likely need larger valves as well. That's not going to let you burn much more fuel.
Really forced induction is the simplest and best way to get more power from a diesel. However Seawalkersee did a supercharger, the only downside he had was the noise. That would give you off idle boost, and turbo power numbers. Granted it wouldn't be bolt on like a turbo, but it wouldn't cost much more out of pocket. Also if it ends up adversely effecting your highway mileage, you can clutch it.
As far as raising compression. That'd likely be more money than stroking it, if it is even possible. An IDI is already absurdly high compression, and because of the pre-cup I think you're simply out of piston travel. I mean they already protrude into the head. The pre-cup is really the only air space left at TDC. That and it would only get you a little more torque, and only just a little.
Diesels are a very simple equation. Your power depends on how much fuel you can burn. How much fuel you can burn depends on how much oxygen you can get into the cylinder. To get more than about 150-175hp out of these motors, you simply have to force more air in there. A turbo will push more, and do it more efficiently; but a supercharger will do it instantly.
That's my two cents.