After supporting about 200 swaps here is my opinion. I will limit this the Gen IV engines since they are emissions compliant and make the most sense in a JK. I will also assume you are running a 6l80 transmission since it is very strong, adaptive, low friction, low heat , inexpensive and available. The 6l80 has a 4:1 first gear and .6 OD which is key to performance, economy and gearing. Guys with 5 speed Chrysler transmissions think they work great compared to the 4 speeds, then drive a 6l80 and feel the difference.
With such a low first gear you can run one size taller gear and still launch a heavy JK hard; then cruise 2,000 rpm @ 70 mph getting reasonable fuel economy in the second OD gear.
There are 3 basic engines to choose from based on performance vs cost, the 5.3, 6.0 and 6.2.
While a great engine the 5.3 is usually not the best choice for our JK's. The 5.3 is only 1.5 liters larger than a 3.8 and has less torque than the other engines. Torque is what hauls your JK around, up hills, fighting headwinds, high altitudes, etc. The larger displacement engines simply have more torque; this means they are more efficient in heavier JK's.
Going to Moab @ 70 mph at 7,000 feet fighting a headwind up a hill is a lot of load on the powertrain; especially in a lifted JK with a lot of drag. The 5.3 will hold the speed but it will downshift, it will go open loop into performance enrichment. This means the 5.3 is spinning faster and running richer, approximately 12:1 in OL.
A 6.0 or 6.2 will hold a higher gear spinning the motor slower, the engine will stay in closed loop running off the O2 sensors with an AF of about 14.2:1. Would be about 14.7:1 but we run alcohol in the fuel so stoich is a bit lower. In the end the larger engine is more efficient in a heavy JK as well as more pleasant to drive without the downshift. A 40" wheel/tire combo can weigh 200 pounds x 4 = 800 pounds so available torque is critical.
So is the 5.3 useless - no. In a light JK with minimum lift and 32" Rubicon wheels and tires the 5.3 is great and can return 20 mpg on the highway. The key is light and low drag, plastic fenders, bumpers, etc.
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