How to swap an LS into your CJ

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Supreme Leader
Jun 7, 2016
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People's Republic of Kalifornia
Over the course of the past 8 years, I have been slowly getting my CJ running after swapping in an LS1 motor. I will do my best to consolidate as much knowledge relating to that process in this thread. There is an exorbitant amount of knowledge and information at

There are more LS motor variations out there than I can keep track of. Keeping this post updated with all of the different variations will be impossible, so I will give as much knowledge as I can and leave it at that.

The aluminum blocks are plentiful. The LS1, LS6, LS3 and so forth all have aluminum blocks and heads. The LS1 and LS6 use a cable throttle body compared to the LS3 using an electronic throttle body. This is one of the differentiating features between a Gen 3 and Gen 4 motor.

The LS1 is likely the most popular and available. It is available in the Trans Am and Corvettes. The LS1 makes more power than torque, but I believe it has the most aftermarket support.

The LS6 makes more power and torque than the LS1, and came in Corvette Z06 and the Cadillac CTS-V. One benefit of this motor that I know of is that it uses an internal PCV system instead of external such as on the LS1.

There are many truck motors, and I do not know a great deal about them. I do know that they are primarily 5.3L and use an iron block with aluminum heads.

***Note*** I know that the truck motors have different engine accessory spacing than car motors. So, you cannot install a truck power steering pump on a car motor without swapping to all truck accessory brackets. Also, the car intakes will not fit with truck accessory mounts. It's either all or nothing, or a very custom application.

When I was searching for a new intake, I found out the Chevy Trailblazer SS 6.0L intake makes the most torque of any other LS intake.
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After searching for a 5.3L truck motor, I wasn't able to find any for a decent amount with low-ish miles. So, I settled for a 98 LS1 out of a Trans Am with some work already done to it.


I chose this motor because it uses a cable throttle primarily, and because it would bolt to a bell housing I had laying around. This would later change anyway, so I would recommend against using that as a decision point.

Some short comings I have discovered about this motor is that the 98 is kind of a bastard child of the LS world. From 99 and later, many things were more standardized across a lot of cars. The primary issue I ran into was computer and wiring harness selection. The 98 uses a special computer and does not have much aftermarket support.

The motor mounts I chose are very adjustable, but they were very expensive and they are pretty bulky. If repeating this swap, I would not choose these mounts.

The headers I originally chose did not fit with my motor mounts. I do not remember the brand but I believe they were from Advance Adapters. You can see the Novak motor mounts I mentioned earlier.

I ended up returning them for a set of Edelbrock short tubes from Summit.

These headers have served me well so far, but they also have some short comings. When I installed my hydraulic clutch, the down tube ran directly into the slave cylinder. In hindsight, I would choose a different set of headers that send the collector straight down instead of angled back like pictured above. I have heard people have lots of success with factory Corvette manifolds.

The radiator I chose is from Advance Adapters. This one does not have provision for a trans cooler but they do offer one that does.

This radiator was advertised to work with a narrow frame CJ with a Gen 3/4 LS motor. The advertisement lied. Neither outlet on the radiator matched my water pump. I had to splice two hoses together to get the two different sizes to work.
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The transmission I chose is the Muncie 465. It is a 4 speed with a granny 1st, so essentially a 3 speed. Working with the transmission itself was fine and I would recommend it for anyone who is planning on a dedicated off road rig. If you have any plans whatsoever of taking your Jeep on the highway, I would highly recommend something with an overdrive such as an NV4500.

To adapt the LS1 to the SM465, I used a kit from Advance Adapters. This kit included a new flywheel and Centerforce clutch kit. It worked well, and I would recommend it.

To adapt the SM465 to the Dana 300, I used a kit from Novak. This was a straight forward kit and I would absolutely recommend it.


In this last picture you can see the Novak tcase adapter clearly, and it includes a nice transmission mount.
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From what I know, the computer / harness is swappable from year to year, but it will require some splicing depending how deep the rabbit hole you decide to go. I elected to buy a 98 computer and harness to match my motor. As I stated in the first post, this is one reason I would recommend 99+ since they have a better / small / more available computer system. The 98 uses a flimsy plastic fender mount for the computer, and I have been through 3 of them so far. After this one breaks I will likely fab something up out of aluminum. One recommendation I have regarding mounting the computer is to not put it on the fender. Mount it either inside the tub behind the dash, or on the firewall near the battery. That way when you are working on the motor you can remove the fenders for easier access to literally everything.

Little did I know, the harness I ordered was the entire harness for a complete 98 Trans Am.

I bought a computer from a guy that had a race tune on it, so it needed flashed. I had the harness trimmed and the computer flashed by a company called wait 4 me performance. They were able to delete a lot of unneeded things from the tune and also removed the two rear O2 sensors from the harness and tune. They did a great job and I would recommend them.
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