Tested at the PCM plug so wire doesn't seem to be damaged. Battery is good, starter is not dragging. Doesn't start immediately like it usually does, but it does start after a few seconds and runs rough. Really puzzled. Usually good at troubleshooting, but I don't know where to go from here.

 

Did you replace the timing set on the replacement engine? Wonder if you got the wrong cam gear.... Yeah, I know, the PCM is whining about the crank sensor, however, I have seen stranger things happen. An improper cam sensor signal my confuse the PCM, and it sets the crank code instead.