2002 Ford Taurus Idles rough and hesitates on slight press of gas pedal?

I have a 2002 Ford Taurus regular 3.0 engine. My car will hesitate upon slight acceleration. Also will not pick up speed or shift properly. My transmission is in good shape so Id like to rule out that.

I have replaced the spark plugs, wires, pcv valve, air filter, oil, ignition coil I used fuel injector cleaner on a 1/2 tank of gas as well. Only thing I have yet to replace is the Crankshaft sensor.
Car shows fault codes
P0316
-Crankshaft sensor defective
-Check connector and wiring to sensor. (have not done yet)
-Check trigger wheel for damage. (have not done yet)

P0303
-Cylinder Misfire on #3
-Ignition system (spark plugs, ignition wires) **replaced these already
-Vacuum Leak (No idea what to do here)
-Injector Fault (bought fuel injector cleaner w/ 1/2 tank of gas)
-High or Low fuel pressure (No idea what to do here)

The two codes could be connected if there's an issue with the crankshaft position sensor tone ring (if it has a damaged tooth), giving a false signal to the pcm for a cylinder 3 misfire. Start by diagnosing/ repairing the p0316 first, take a good look at the tone ring. Or pay $100 for diagnosis at ford.

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