Camshaft Sensor Code

[My Sons Explorer]

Need some help, my son's 2002 explorer ever since I put a new motor (out of a 2001 sport trac) I cannot get the camshaft sensor code to go away. Engine starts and runs great, no bogging down, no idle issues, and all of the wires look good. What could it be?
One thing to note and not sure if this will make a difference but the left side head is a 2002 and the right side is a 2001. The vehicle is flex fuel but the motor is not.

Appreciate any advice I can get

 

[My Sons Explorer]

Awhile back I did a valve job on the left head, after putting it back together I found this small rod laying on the table, can't figure out where it goes.
I've looked the head over several times, if this goes in the head somewhere could this be why I can't get rid of he Camshaft sensor code