I recently have been having an ongoing issue with code 0303 which is a misfire code on cylinder #3. With me thinking the worse, I immediately did a compression test on cylinders 1 with it being 130 PSI and holding. Cylinder #1 being 130 PSI and holding, cylindder #5 being 128 and holding. I also checked cylinder #8 for just because and it was 125 PSI and holding. So im pretty sure I can rule out any mechanical issues at this point. I also used my mechanics stethescope to listen at the injectors and could hear the solenoids clicking open and shut on cylindder #1, 3, 5, 7 and 8. Another thing I did was put a in-line spark tester on cylinder #3 and the thing is getting fire, good fire too.
The mis-fire is pretty much intermittent and usually happens when you put a load on the motor (accelerate). The longer the motor runs the worse it gets.

 

Is this a 5.9 engine? And what parts have you replaced already?

 

I read another post you started. The P0203 code which is a fuel injector code. And this will also cause a misfire code on number 3 cylinder. Switch the injector to number cylinder. If the injector is bad, your misfire should move to number 2 cylinder. If it does, replace the injector.