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2003 Civic DX. Getting a p0336 code and associated issues after replacing ECU

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Old 06-28-2019
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2003 Civic DX. Getting a p0336 code and associated issues after replacing ECU

2003 Honda Civic DX, 125000 miles

Had a Honda dealer swap out the ECU after a loose altinator fried it. Unfortunately, they did not tighten the altinator and the second fried almost immediately. I swapped it and the key set with a salvage one with close to the same miles as my car as the garage is 300 miles away. Shortly thereafter, the maintenance required light came on, got a code for #3 cylinder misfire and then a crankshaft position sensor code - P0336. I have changed sparkplugs and a cracked ignition coil on number 4. AI will be changing out number three when the part arrives next week. The car has started to buck and stall and I want to bring it to a local mechanic, but he isn't set up to do this type of diagnosis (out in the middle of nowhere where old trucks are the norm). Is it possible that the swapped out ECU is the issue or could that have cause the crankshaft position sensor to fail?
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