If the new engine has extended clearances it will make noise for the knock sensor causing the issue. How does the engine sounds when running? Can you please shoot a quick video with your phone so we can hear the noise, that would be great. You can upload it here with your response.
If the engine is quiet I have seen a bad ECM cause this problem as well. I would try a used/rebuilt unit.
Check out the diagrams (below). Please let us know what happens.
Cheers, Ken
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Thursday, November 29th, 2018 AT 12:15 PM