A while back the air cleaner box clip broke and the intake was pretty dirty when I noticed what had happened. It had started sputtering like it was missing a cylinder almost and RPMS would drop and it would idle rough. Now that is has warmed up to about 80 degrees during the day it takes longer to start as well as feeling like it is putting out only half power for about the first mile of driving. Then after that first mile it feels like more cylinders are starting to fire and then the motor is putting out noticably more power. The fan clutch was bad and I changed that but there was no change noticed. Also changed the PCV valve at the same time and again zilch. Does anybody have any idea what to check from here or have had this type of issue?

 

I would start with a fuel pressure test, specifically watching the leak down rate after the pump shuts off. You should see ~60psi with the key on and the pressure shouldn't drop below 50psi after it shuts off. If the pressure falls to zero, you have a fuel leak.

The most common leak point for the CPI engines is the FPR (fuel pressure regulator) located inside the intake plenum.