2003 5.4 truck is missing bad but is not throwing any codes, have replaced fuel filter and cleaned mass air flow, is there any way to check each individual cyl?

 

have you thought about a tune - up ?? Plugs COP's ... most likely a mis-fire ... what do you want to check on each cylinder ?

 

A bad coil doesn't necessarily have to throw a code I would go through and unplug each individual coil
No change to the running motor means the coil is bad if it gets worse it is working or try to get the truck to throw a light to pin point problem area