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did you use the same size motor??
I would have stripped down the donor motor and changed over all the externals from the bad motor to the donor motor. then you could use the harness that was with the truck.
no you cannot upgrade the ignition switch to accept the 2006.
did you use the complete harness from the 2006??
the harness is completely different. does the pcm light up the check engine light with the key on???
then the pcm is working. the 2006 had a chipped key. with you using this motor and pcm, you need someone to access the pcm and take off the security for the key.