cylinder 2 and 3 misfire P0302 & P0303

2008 Chevy Aveo (4 door sedan), automatic transmission.

Car was wrecked. As a result the engine was replaced. Car has 75K miles. Was told the engine had 25K miles.
Check engine light comes on after driving on the highway at about 60MPH for a min or two.

We have replaced the plugs, wires, and solenoid. Also, due to other codes, replace the O2 (upper and lower) sensors.

The engine runs great. No hesitation. No loss of power.
Plugs are clean - no oil.
Engine runs smooth and quiet.
Car drives great.

Is there a way to narrow down the other potential causes with out replacing part after part?

Best I can tell from research online is other potential problems are:
Crank Shaft Position Sensor
MAP (Manifold Pressure) Sensor
Valve adjustment/replacement
Gaskets
Various wiring issues
I've even heard of transmission causes, intake manifold, and dirty injectors.

Assuming the 2 & 3 plug wires are in the correct order, what plugs did you put in? I have tried several different plugs, but imho they all suck but the NGK.. thats not an advertisement, but i ran autolites for 1 trip home, barely made it without misfires.