I think you need to look at the differences between a 2014 and 2008-10 motor.
I came up blank trying to figure out if the crank tone ring is different but did find one place that sold a 58 tooth ring for 2009-2012 motors and a 58 tool ring for 2013+. Might be the number of bolts it uses, but could be the spacing, too.
And the VVT motor was introduced in '09 (at leas as far as I know), but your PCM spans that year. That feels wrong.
I would bet the trouble you are having is all due to the PCM not working with the components on the motor.