Hi, I'm new to this forum and decided to sign up because I took on a project that was a little over my head. I did my first motor swap and now that it's in I am having problems. I tried everything I could think of and was hoping for some help. Thanks.
I swapped 4.0 junkyard motor from a 94 wrangler into my 94 cherokee because I drove mine through a deep puddle, hydro-locked it and threw a rod through the block. I used only the block and the head from the donor motor. Everything else is from my motor. Upon completion of the swap I started the motor. It gave me trouble starting up but I was able to get it turned over. The motor seems to idle a little bit rough but it does idle and run without stalling. As soon as I try to give the motor gas it spits and sputters and does not seem to take the gas. When I back off the throttle the motor pops and backfires.
I first checked all the vacuum lines and think that they are all ok. With no success I ran the error codes and got back a 21 (bad o2 sensor), 23 (air intake temp sensor), 24 (throttle position sensor) and 41 (open or shorted alternator). I assumed that since all these sensors work based on proper voltage an open or shorted alternator could be throwing all of their readings off. I had broken one of the grounds on the back of the alternator during installation but re-grounded it on another spot on the alternator. Assuming this could be the problem I ran this ground directly to the chassis and had no luck so I then replaced it back to it’s new location on the alternator. I then hooked the truck up to another jeep with jumper cables so that I could be certain the system had proper voltage and still the motor gave me the same result.
My next step was to replace the throttle body (because this would swap the TPS) and the air intake temperature sensor with the one from the junkyard motor. I swapped these two sensors in one at a time and still encountered the same problem. So I put my original sensor and TB back into the truck and moved onto my next step.
I went up and bought a new o2 sensor and put that in the truck. This didn’t fix anything either. Starting to get desperate I decided to do a full tune up even though I was using a fairly new distributor cap, rotor, wires and plugs. I replaced all of these and still have the same result.

 

A couple of questions;

Have you made sure ALL of your grounds are connected?

Did you use the XJ flex plate or did you use the TJ flex plate?

Has the distributor been removed on the donor motor? If so I suspect indexing could be a issue.

 

All of my grounds are connected. By flex plate you mean the plate that is between the transmission and the block? I used the one from my cherokee. The distributor has been removed. I had to use the one from my xj on the tj motor because the one on the tj was damaged

 

You mention backfiring. Backfiring in the intake usually is caused by a "lean" fuel condition.

1. Test your fuel pressure with a gauge. No shortcuts. You should have 31 psi at idle. Then disconnect the vacuum line leading to the fuel pressure regulator (be sure that line is pulling good vacuum) and the fuel pressure should jump up to approximately 39 psi.

2. Test your MAP sensor. Again, verify vacuum line leading to it.

Start testing your way to a solution here..........

 

You need to make sure the distributor is indexed properly. I'll bet its off by a tooth or two and regardless of what others will tell you it does make a difference.

The procedure;

ROtate the engine until you have #1 piston at Top Dead Center, "compression stroke"

Mark #1 plug wire terminal on the distributor housing and pull the cap. If the rotor is pointed to #1 terminal or just before it you are off a tooth(or more). The rotor should be just past #1 terminal(clockwise) or on the trailing edge of #1 terminal.

If you need to re-index; pull the distributor out and re-install it. Remember as you drop in the dizzy it will turn clockwise as it meshes with the cam gear so compensate for that(you may also have to rotate the oil pump drive to mesh with the distributor shaft as well, I do this with a long screwdriver)

 

Thanks so much for your help guys. It turned out that it was the timing and once I got it adjusted the motor ran perfectly.