I felt the same way about my '94 3500 auto with 4.10 rear end when I first got it and put it to work in 2005. Here's what I went through to get mine to make power like I thought it ought to.
Get the valves adjusted, it's recommended every 24,000 miles.
Make sure the injection pump is timed properly with the engine. If the timing is off, then it's not injecting the fuel in the cylinder at the right time.
Make sure turbo and waste gate are functioning properly. My waste gate was stuck. I was getting 17 psi boost but the truck couldn't pull a greased string out of a cats butt! With the waste gate stuck, the engine was working against back pressure. It felt like my boss's Chevy 3500 with a 350 had more power! After the waste gate was fixed it was like a different truck.
Then I put on a BHAF, then a 4" turbo back and both these showed positive results. Next I got a TST power kit with new fuel plate, boost elbow, AFC spring kit, and also I added a Banks Twin Ram intake. All of this drastically improved the power. I'm getting nearly 30 psi of boost and I can accelerate going up hills now, where I'd lose speed before. And it doesn't smoke like crazy either. My truck has a 9' Reading tool body with a cover over the center section that has 60" from the floor to ceiling inside. The top of the body is 9'3" tall and the body itself weighs 2500 lbs. So my truck is always carrying a load.
I think next on my agenda with be a new transmission and TC, leaning toward a Firepunk Towmaster right now. I feel like the truck is making the power it ought to be, but a lot of that power isn't making to the wheels because of the sloppy TC and transmission. I also have a governor spring kit that I got from TST, that I'd like to put in as soon as possible.
After all these mods I'm a lot more happy with the truck. And wouldn't trade it for anything. My wife told me to get rid of it and get a new 2017 chassis cab but I'd rather have this one for a work truck! Hope this helps.