P0303, Rough Idle + Vibration, High Revs in 1st Gear?
 

Car idles a little off, misfire on cylinder 3, already changed the spark plugs. Could this be a bad coil pack? If so, how would I go about testing it?

I am planning on cleaning the throttle body after reading a few other threads on the forum here.

I've also found that I have to rev the engine quite a bit 1200-1500 to get it going in 1st gear, otherwise it starts out very jerkily. Is this normal for this transmission, or should I look at possibly doing a clutch replacement / throwout bearing at some point? I have noticed some noise in neutral that stops when I push the clutch in (minor squeaking)

Thank you for any advise that you can offer. I should mention that this is the first car I've ever owned with a gasoline engine...

Don't know own about the rest of the stuff you stated, but to diagnose the coil packs, switch the #3 coil pack with another one, and see if the misfire follows it.

I did this and the code followed to the new cylinder. So, I went ahead and replaced all of the coil packs with OE parts. The old coil packs were pretty badly damaged when compared to the new ones.

Now I have new codes.

P0300, P0302, P0303, P0441, P0455

I cleared those codes and reset the ECM. When the car first starts after sitting for a while it will idle all over the place and then settle down. During the drive regardless of how long, no issues present. It just seems to be misfiring at startup and immediately sets these codes.

Steps I've taken since replacing coils: Remove all 4 iridium plugs and re-check the gap. It is within factory spec, .043" on all 4 plugs. Plugs do not seem fouled so I doubt that the car is burning oil.

HOWEVER - You can certainly smell the exhaust at idle. Could my car be running rich? I am averaging 21mpg highway, 17mpg city, which seems terrible compared to EPA estimates. I'm not hot rodding the car and it's bone stock...

Is there anything else I can check? I've already verified that the gas cap is tight and I don't see that causing a misfire unless the fuel system is completely pressurized...?

Get a obd2 scanner and check the fuel trims.
If they are over 7 +/- then there is a problem.
Either an exhaust leak before the o2 sensor, or an intake leak after the maf sensor.
Dirty maf sensor can also cause these problems too.

your 400 codes are evap.
Its possible the valve is leaking and stuck open.
Causing extra fuel fumes to be suck in. that will kill mpg and can cause misfire due to the car taking in fuel and air thats not meter to the ecu.

UPDATE: Car has a blown head gasket and possible damage to the head. This was the problem all along. Hopefully the dealership I purchased the car from stays true to their word about fixing it for me.