"When forums say things like, "crank the engine" is that talking about cranking it by hand?"
It means, turn the key in the ignition to "start".
".. when I'm turning the key to start the car, should I be pushing on the gas pedal... I figured that would flood the engine if its not firing."
This is not the normal procedure for everyday starting. However, in your case, as posted previously, you should. If the engine is flooded, this will cause the injectors to shut off. If the cylinders has lost compression, this should help regain compression. And if there is less fuel than is necessary to start (air in the fuel injectors), this should also help start the engine.
Note that almost all of us who have done a UIM/LIM rebuild have experienced the "takes a long time to start after putting it back together" syndrome.