how do I make the rear end stiffer?

To raise the back of your truck you are going to have to replace the shocks and springs to give it more height in the back. It may be that the shocks and springs need to be replaced anyway as the car is 12 years old, but you may need to install bigger shocks or springs to "jack it up"

replace the old shackles with longer ones

shocks wont help ride hight(unless air shocks) put in an add-a-leaf it will fix your problem

Different shackles or lift blocks if your axle is below your leaf springs.