I bought a 2000 cherokee with 4.0/AW4 that was knocking and ran very rough. I bought a used motor and swapped it in. I did tear down the old motor and found cylinder 2 scored pretty bad.
I fired up the new-used motor and it purred like a kitten for 10 minutes. Great oil pressure, got up to operating temp and stayed there. I drove it 100 feet and it sputtered and died. Started back up and it has a random knock that comes and goes. The engine runs very rough when it is knocking.
Weird thing is, this is exactly what happened with the old motor. I had picked up the jeep on my car hauler, never ran it(I was told the engine was blown), and brought it home. When I got it home I tried to start it, it started right up. I drove it the same 100 feet and it did the exact same thing that it did with the new engine.
-I have a new crank sensor
-good fuel pressure and all injectors working
-new spark plugs after knock started, old ones looked good
-cam sensor is positioned properly
-no check engine light
-torque converter bolts are tight
-wiring harness looks good, I've inspected the whole thing
Could I have water in the fuel? Bad ecm? Any other ideas?

 

Check the heads on both. Could be a cracked head allowing coolant to get in. 00 - 01's are known for this.

 

Tommy54, a good test for water in fuel is to pull the test port on the on the fuel rail, put a rubber hose on it and jump the pump relay, and pump into a gallon milk jug. Let it sit out of the sun for about 2 hours and check it. If it has water, it should seperate into layers in the jug. A fire extinguisher ain't a bad idea to have on hand.

 

wireing to down stream o2 not touching to ground bye tc drive shaft area is it

 

-The first motor had the notorious garbage head, although it doesn't have a crack that's visible. This one is from a 99, and has the 0631 head.

-I think I will drain all the gas. Might as well, the jeep sat for a couple months before I bought it. Who knows what might be in there.

-I will check both o2 sensor wires. I hadn't thought to check the downstream sensor.

Is there anything in the torque converter that could cause a knocking sound? I tightened the bolts to the flexplate. I can't believe that I bought a motor that does the EXACT same thing as the old one. It has to be something besides the motor itself. I am trying to be optimistic here.

 

A cracked flex plate could make a knocking as well, idk if that would cause it to run rough though.

Take some video and post it up, you may get more ideas if people can hear/see what's goin on.