I have a 91 4Runner with 4" MC Leaf's in front and 5" in the rear. With a moderate load (including the spare tire and carrier) it has a serious sag in the rear and I'm constantly bottoming on the bumps stops. Have others had a similar experience? What have others done to correct this issue?
Thanks in advance 
I've got Marlin's 5" HD springs in the rear of my 93 4Runner with 6" shackles (and Marlin's 4" front springs with 4.5" shackles. I am really happy with them, but I had to make some simple adjustments as they broke-in.
So after a few trips in 2008, I realized that the springs were beginning to break-in, and I noticed that my rear shackle angle had relaxed a bit too much since the install, requiring relocation of the rear shackle hanger backward to accomplish what SocalWheeler71 suggested without changing to a longer shackle. You can ask others who have wheeled with me, I carry a lot more than a moderate amount of weight in my Runner, and I have a full size spare and an internal cage which adds even more weight.
After a slight relocation backward of the rear shackle hanger, I have had no problems with the rear set up. Despite being HD, my rear springs flex really well IMHO. I definitely think that the HD springs are what keeps me from sagging, and I tell anyone who is rear-leaf-swapping a 4Runner that they should get Marlin's HD 5" springs with their regular 4" springs in the front. I know some guys suggest that Marlin's springs were designed only with a 4x4 P/U's weight in mind; therefore, Marlin's springs do not work well with 4Runner applications. I don't think this is all together right because Marlin does offer the HD rears specifically for heavier rides, which have worked well for me, and I also know that there are a lot of people, including Marlin himself, who carry a lot of weight in their P/U truck beds and also run his standard 4" and 5" springs without any issues. I think you might just need to adjust your set-up. Are you running the HD springs? How long has it been since your initial install? Post some pics.
Here are some pics of mine; it sits pretty level here on the street:
It's certainly not the lowest thing in the world, but here is one where you can see my shackle angles and my springs, which you can tell are still breaking-in, and which is just fine.
Here is one from Moab:
