Keep in mind each cylinder has a compression stroke and an exhaust stroke. So the motor is not always at Top Dead Center just because the crank lines, line up. It could be 180 off. The crankshaft has to rotate twice to complete one full combustion cycle.
Down,
Up,
Down,
Up
Intake,
Compression,
Ignition,
exhaust
So the crank will line up twice per cycle, and will alternate TDC, 180 OFF, TDC, 180 OFF, TDC, 180 OFF, TDC, 180 OFF, etc etc etc
The cams spin at half the speed the crank does. Its not a 1:1 ratio. For every 1 rotation of the crank, the cams spin 1/2 way around and vice versa (1 camshaft rotation equals 2 crank rotations) so that is why the crank mark can line up, but still be 180 off.
Look at this image to help clarify what I am talking about. Notice that each time the crank mark is at the bottom what is happening in the cylinder can be one of two different things. That is why the crank can be in the right "spot" but still be need to be rotated one more time. 180 off is in regards to the combustion process (or cam position), not the crank being physically turned 180 the wrong way. That sometimes confuses people. This is why the cambar has different sized holes/pegs, so it will only fit on one way, and not when the motor is 180 off:
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