I checked the oil when this happened and it was good, doesnt seem to have any oil leaks. It also shot a code out saying I have a misfire on all 4 cylinders.

 

Sounds like it

 

No, does not sound at all like rod knock to me.

Rod knock as a more metallic ringing sound, higher pitched. Yours is a more deeper thud.

I'd try things like:

Temporarily remove serpentine belt, see if noise persists (rules out all belt driven accessories and crank damper)

Use mechanic stethoscope to try and isolate if noise is front, back, top, bottom, etc.

See if noise changes when pressing clutch

Did anything change recently, any work done, etc?

 

I recently got a clutch installed

 

Does the noise change when you press the clutch pedal in?

 

I was wondering about the clutch. Because it sounds to me like something whacking bell housing or resonating in the bell housing as engine turns.

 

When the clutch is pressed in the noise gets softer.

 

Can you feel the vibrations on the shifter lever? Does is change when you press the clutch pedal in?

 

Yes I feel the vibrations on the shifter, the vibrations on the shifter get less aggressive when the clutch is pressed.

 

On second thought, the clutch thing maybe coincidence. What CEL code numbers are you getting?