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Re: 5.3 Gen 3 - Misfire/rough idle
I would start with a basic compression test since this engine is new to you.
Fuel pressure/filter and spark plug condition next.
As you stated, the harness is butchered get that straightened out after checking the easy stuff 1st.
Can you post a pic of the engine? There are a bunch of sharp dudes on here that may pick up on something they see.
Hope this helps!
Blake
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