There aren't many fivers made today that don't already have the axles below the springs. In a 2014, that's probably not going to help.
OP, you still didn't say how much clearance you have between the fiver overhang and the top of your bed rails. You really don't want to go too close there. Should be at least 6", definitely not less than 5". Since you already lowered the nose 3", makes me concerned about that bed clearance.
Top side clearance won't be an issue. Ignore that stuff above. Just make sure you know how tall you are, and pay attention to clearance signs on the road. You won't end up greater than 13-6, so don't worry.
When measuring how out of level you are, don't measure at front and rear. Measure to the bottom of the frame, on level ground. Measure at the front of the base frame, and between the axles to the base frame. You will find that you are much less than 6" out.
To determine if there really is a problem, or not, head to the scales and measure the weight on each axle. Unless it is badly unequal, you don't have a mechanical issue. You might still have clearance issues.