4.0 Engine Replacement in my 06 TJ

[Superjoe]

After some diagnosis at my friends shop Bavarium Autosport‘s it looks like my engine needs to be replaced...
Engine failed compression test and leak down found two cylinders around 80% the others were around 30%. Surprised this thing still ran.
My friend found two injectors intermittently fully open. Looks like over fueling caused the two cylinders to fail. Failed injectors and PCM.

Originally I was planning on saving for a year and replacing the engine with a stroker. Looks like the Jeep can’t wait that long. After a bunch of research and checking pricing online for engine options. I decided to replace the engine with a used engine from a local Jeep wrecker J&W Jeep. The engine has 41k original miles from a 2006 Rubicon. It was $1850 including a set of Exhaust manifolds (Headers Leaking). I felt like this was a good price for an engine that should last me a few years until the stroker.

I have built out a few other vehicles in the past and I have over 20 years in the automotive dealership world. I might be going a bit overboard for some. The Jeep has 170k miles on it, I am planning on replacing quite a few parts while the engine is out. Most of the parts are going to be OEM with a few exceptions that I have not seen the value in spending the extra money on. Any input is welcome as this is my first Jeep.

Below is the parts list going along with the engine replacement.

OEM Parts
Radiator
Water Pump
Serpentine Belt
Idler Pully
Belt Tensioner
Intake/Exhaust Manifold Gasket
Crankshaft Damper
Engine Lower Gasket Package- (Oil Pan, Timing Cover Gasket, Water Pump, Oil Pump Gasket)
Front Main Crankshaft Seal
Engine Mounts
Heater Hoses
T/Stat Gasket
Throttle Body Sensor
Crank Shaft Sensor
Coolant Temp Sensor
Air Temp Sensor
MAP Sensor
Oil Pressure Sensor
Ignition Coil Assy
P/S Pressure and Return Hoses
Coolant
Oil Filter

Aftermarket Parts
Valve Cover Gasket- Fel Pro
Radiator Cap- Stant
T/Stat- Stant
Radiator Hoses- Gates
Fan Clutch- Hayden
PCM- Wranglerfix
Fuel Injectors- Precision Auto Injectors (Rebuilt)
P/S Fluid- Lucas
Spark Plugs- Autolite XP985

 

[Claytone]

I didn’t see the rear main seal on the list, but I’d assume you’re doing it too.

 

[JKP]

P/S fluid for an 06 is ATF+4 if you have OEM pump and box.

 

[Superjoe]

Yes, rear main is getting done with oil pan.
Thank you for the advice on the P/S fluid.

 

[Cross-Threaded-06TJ]

I didn't see 5.3 on the list either. Or 6L80E.

 

[Superjoe]

I didn't see 5.3 on the list either. Or 6L80E.

I was thinking Hemi at one point but I think the numbers from the stroker will do.

 

[Cross-Threaded-06TJ]

I was thinking Hemi at one point but I think the numbers from the stroker will do.

Excellent.

 

[Weasellee]

If replacing the motor mounts maybe look at the upgrade available and/or a 1” lifted mount. I used the M.O.R.E. 1” raised Bombproof with rubber bushing in lieu of poly bushings. Good luck and I’d buy a 41k mile engine for 1850 all day

 

[Superjoe]

If replacing the motor mounts maybe look at the upgrade available and/or a 1” lifted mount. I used the M.O.R.E. 1” raised Bombproof with rubber bushing in lieu of poly bushings. Good luck and I’d buy a 41k mile engine for 1850 all day

Thank you! I haven’t researched these. Is this needed if you have a slip yoke eliminator?

 

[Weasellee]

Thank you! I haven’t researched these. Is this needed if you have a slip yoke eliminator?

Not 100% sure. The bombproof mounts are available with or without the 1” raise.

 

[Superjoe]

Old one is almost out!

 

[Rubicon88]

Replacing the gaskets and rear main isn't a bad idea with all that removed....
I'm assuming your (new to you) engine is complete with all sensors and wiring harness all ready to go...???
If so I wouldn't just replace all those sensors by default.
The junk yards are good at testing and grading parts including engines. The boneyard's bread and butter us selling used engines and transmissions to garages like me. If they list an engine as being in excellent running condition...grade A...whatever...
If it was good running engine a gasket refresh is fine but doing all those sensors en masse might wake a sleeping dog or two or three.
In other words you don't want a situation where you've got a quagmire of misfires, etc.. and installing all new sensors could be a pita figuring out which one(s) is not playing well with others. If the new to you engine is complete...do your gaskets and rear main, change your oil, filter and plugs and fire it up.
On the spark plugs... I would use
NGK ZFR5N.
Especially starting off with a new to you engine it's always a good idea starting at ground zero. Ground zero meaning an OEM part. That is the plug OEM recommends.

 

[Superjoe]

Replacing the gaskets and rear main isn't a bad idea with all that removed....
I'm assuming your (new to you) engine is complete with all sensors and wiring harness all ready to go...???
If so I wouldn't just replace all those sensors by default.
The junk yards are good at testing and grading parts including engines. The boneyard's bread and butter us selling used engines and transmissions to garages like me. If they list an engine as being in excellent running condition...grade A...whatever...
If it was good running engine a gasket refresh is fine but doing all those sensors en masse might wake a sleeping dog or two or three.
In other words you don't want a situation where you've got a quagmire of misfires, etc.. and installing all new sensors could be a pita figuring out which one(s) is not playing well with others. If the new to you engine is complete...do your gaskets and rear main, change your oil, filter and plugs and fire it up.
On the spark plugs... I would use
NGK ZFR5N.
Especially starting off with a new to you engine it's always a good idea starting at ground zero. Ground zero meaning an OEM part. That is the plug OEM recommends.

Thank you for your recommendation and sharing your experience with the junkyard engines. The engines have always worked out well for me as well. The engine is not complete with all sensors and harnesses. It has a couple still on. I understand your logic with the possibility of a defective or misboxed part. Being that all parts are potentially 15 years old and everything is apart I am going to replace them. The sensors didn’t cost that much. I am interested with your spark plug recommendation. I replaced the plugs with NGK before finding the engine needed replacement. I chose the NGK’s because they were factory. After reading all of the posts on the forum I decided to go with the autolite platinums now. Have you had a bad experience with the plugs?

new/used engine

 

[Rubicon88]

Thank you for your recommendation and sharing your experience with the junkyard engines. The engines have always worked out well for me as well. The engine is not complete with all sensors and harnesses. It has a couple still on. I understand your logic with the possibility of a defective or misboxed part. Being that all parts are potentially 15 years old and everything is apart I am going to replace them. The sensors didn’t cost that much. I am interested with your spark plug recommendation. I replaced the plugs with NGK before finding the engine needed replacement. I chose the NGK’s because they were factory. After reading all of the posts on the forum I decided to go with the autolite platinums now. Have you had a bad experience with the plugs?

new/used engine

View attachment 239252

View attachment 239253

Yes...and I put those soecific Autolite plugs under the same umbrella as the Redline fluid change for these notchy ignorant manual trannies.
Mixed results. Works for some....some no change...some have worse issues.

It's your bread but I can tell you this...if someone came in to a Jeep dealer for a misfire let's say a p0304 or similar...if good condition NGK's aren't in there that's the first thing the tech will do is walk to the parts counter and get the oem plug before proceeding.
Again, they work for some and some have issues.

Given you're putting a new to you engine in I'd start as close to ground zero as possible.
Example...
Would you put in a Carquest or Driveworks or Duralast water pump? You can bet there are forum users right now who've used the immediate above...can't find, can't afford oem.. whatever .. and some haven't had issues with them.
You list using a mopar (oem) water pump...
It appears to me you want oem parts that are very important...I'd say plugs are pretty darn important. If you get the urge to swap them later on go for it...but on a new to you engine ESPECIALLY putting on so many new parts before firing...
I'd definitely stick with ZFR5N

Great looking Jeep BTW. How do you like the half cab and how long have have you had it like that?

 

[Superjoe]

Yes...and I put those soecific Autolite plugs under the same umbrella as the Redline fluid change for these notchy ignorant manual trannies.
Mixed results. Works for some....some no change...some have worse issues.

It's your bread but I can tell you this...if someone came in to a Jeep dealer for a misfire let's say a p0304 or similar...if good condition NGK's aren't in there that's the first thing the tech will do is walk to the parts counter and get the oem plug before proceeding.
Again, they work for some and some have issues.

Given you're putting a new to you engine in I'd start as close to ground zero as possible.
Example...
Would you put in a Carquest or Driveworks or Duralast water pump? You can bet there are forum users right now who've used the immediate above...can't find, can't afford oem.. whatever .. and some haven't had issues with them.
You list using a mopar (oem) water pump...
It appears to me you want oem parts that are very important...I'd say plugs are pretty darn important. If you get the urge to swap them later on go for it...but on a new to you engine ESPECIALLY putting on so many new parts before firing...
I'd definitely stick with ZFR5N

Great looking Jeep BTW. How do you like the half cab and how long have have you had it like that?

Alright you’ve convinced me to go stock...
I’ve told 100’s of people the same thing working for dealerships so many years. What kind of person would I be if I didn’t follow my own advice?
NGK ALL THE WAY!

Thank you! I’ve only had the Jeep a couple of months. It started life as demo Jeep for Daystar. Then one of their salesmen owned it for a longtime before me. The half cab kit was put on very early. I really like the look of it. Bed is 4 feet so it’s hard to fit some stuff in there like my bike! Might have to do a CJ7 tailgate swap.

 

[Superjoe]

And it’s out!

 

[Rubicon88]

O

And it’s out!

View attachment 239480

Oh no...wrong transmission..

Good job. Keep the momentum rolling.

 

[Superjoe]

It’s done!