Engine at WOT or part-throttle? The best way to increase low-end torque is with a longer runner, or a smaller diameter runner to the port. Unfortunately most can't do this.
In the case of stock vs new, your best to try and just smooth out the intake with metal pipes instead of calculating length for torque which needs done on an individual cylinder basis. You can go to a smaller diameter intake pipe to try and increase intake gas velocity which would increase torque but only at or close to wide open and it's possible that your intake plenum will just cancel that out. Most log-style intakes tend to do that.
its not the intake pipe between the air filter and throttle that will make any difference, its the length between the throttle plate and the intake valves that will determine the operating characteristics. short runner vs long runner, etc. If you are up for some good reading, do some searches about intake manifold design and what not. Pretty interesting stuff.