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I bought a 2005 Mustang V6 cheap. After getting home with it, I found out why - the block was cracked. Luckily, I found a replacement with only 23k Miles. The tag on the replacement says it was an '06 model. The wiring harness connected to everything just fine, EXCEPT for the 3rd connector on the ECM, so I put the original harness on the replacement. Also, I had to move the flex plate to the replacement motor because the holes for the torque converter were too close together on the newer motor. I replaced all four of the O2 sensors - the wires on them were damaged. I also put a cold air intake on it.
Here's the problem: The car will run fine one time when I take it out, but sometimes, it will be running fine and then drop out. It does this regardless of the speed and gear I'm in, and it will do this from a dead stop. The car does not die though and it starts right up every time you turn the key. When I push on the accelerator, it will kick down to a lower gear, but it's as if someone cut the power in half. Also, if I shift into neutral and hit the accelerator, it seems to momentarily clear the problem. It doesn't backfire but it definitely runs rough. I have replaced the fuel pump (inspected the tank - it was CLEAN), fuel filter, coil, plugs, and wires. I cleaned the MAF and throttle body with the approved cleaner, checked for vacuum leaks, and tested the voltage from the TPS and it seems to be working fine. The car still does the same thing, hot or cold, rain or shine, day or night. The engine light does flash when it acts up - it's throwing out codes for random misfire, left and right bank rich, and left and right bank lean. I also pulled the cats and found they are both empty - I know this will cause some issues, but I don't think it will cause what's happening now. Sorry to run so long, I just wanted to provide all the pertinent details.
 
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