P0016 - Crankshaft Position - Camshaft Position Correlation (Bank 1 Sensor A)
P0068 MAP/MAF - Throttle Position Correlation
P0107 - Manifold Absolute Pressure/Barometric Pressure Circuit Low Input
P0641 Sensor Reference Voltage A Circuit Open
The last thing you want to do is disconnect the battery. That can erase a fault code, but that doesn't fix the problem that set the code. It also erases all the other learned data, and you lose the valuable information stated in the fault codes. The fact the codes set again right away is proof the Engine Computer is detecting these problems. With over 2,000 things it can detect, you need those fault codes to know where to start looking.
Given the nature of the recent service, the best suspect is damaged wiring. First look for wiring harnesses that are draped over the sharp edge of a metal bracket and may have rubbed through to the point a wire is cut or is grounding out. What happens to one wire will also happen to others next to it. Next, look for connector terminals that had corrosion between them, and that got disturbed when they were disconnected to replace the engine. Simply disconnecting and reconnecting a plug can make an electrical problem show up now that was about to occur on its own very soon.
Codes 68 and 107 are almost certainly related. Watch the throttle position sensor's readings on the scanner as you push the accelerator pedal from idle to wide-open-throttle. You should see the signal voltage rise smoothly from approximately 0.5 volts to around 4.5 volts.
Watch the MAP sensor's reading to see what it is with the ignition switch on, engine not running, and what it changes to when the engine is running. Let me know what you find.
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Thursday, March 29th, 2018 AT 2:41 PM