Here are the factors that influence QB accuracy:

1) their accuracy rating (duh)
2) experience and fatigue
3) if the QB is moving, their scramble skill (the faster they are moving, the more their scramble skill comes into play)
4) the distance the ball is being thrown - further distances have less accuracy. This is the only tweak I made recently, previously there was no distance penalty for passes shorter than 15 yards, I changed that because too many bad QB's were playing like superstars with the short passing game. It's possible this still needs to be tweaked.
5) Pressure from the defensive line

4) the distance the ball is being thrown - further distances have less accuracy.

Is this absolute distance or is relative to a QB's Arm Strength?

The 'target' position is calculated based on his arm strength, then the accuracy to that point is impacted by his accuracy with a reduction in accuracy based on distance.