I replaced my '98 Wrangler engine last year with a remanufactured one. The crankshaft position sensor was connected when we pulled the old engine out. DOH...it snapped the sensor off it's mount, and so when we got the new engine back in and running, it was no surprise that it spit out a 1391 error code: "intermittent loss of either camshaft or crankshaft position sensor". So I replaced the crankshaft sensor with a new one. Still the error code. So then I replaced the camshaft sensor with a new one. Still the error code. I reset the PCM, but the check engine light keeps coming on.
So, I'm thinking maybe the wiring harness connector was damaged when we pulled the engine out, or possibly a short? Any suggestions would be great. My smog inspection is way past due now.