In the all these animations of the pistons I see linear motion translated into rotary motion using the crank shaft - but how do you design the pison/crank to always turn clockwise or counter clockwise (based on how you view it, obviously)? Is it possible for the crank shaft to lock up if it's perfectly oriented at 0 degrees?
It is actually possible for an engine to turn the wrong way, this occurs on motorbikes with kick starts. When you don't kick start it correctly (or if the ignition timing is way out), a piston can fire prematurely before top dead centre and force the crankshaft against the direction that the kick lever turns it, this is known as kick back and is about as fun as it sounds when the engine's force goes through the kick lever.
You can design the starter motor to ensure the engine always starts up moving in the right direction, and after that it's "just" a matter of timing (e.g., spark plugs controllled electronically in more modern cars, mechanically in older ones).
> Is it possible for the crank shaft to lock up if it's perfectly oriented at 0 degrees?
That's what the starter motor is for!