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you will have to check compression, have you?
those coils must be checked for power supply, if power is there, then check if groung control from computer is there. coil ground has be pulsating.
also, injectors on those cylinders must check if working.
injectors have constant power to one of the wires and pulsating control ground on the other wire.
if wiring and power is is good, then comuter is malfunctioning.
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Has a scan tool been used to identify specifc cylinder # XXXXX misfires and when it happens on a DATA list? Did you replace the coild specific for cylinder # XXXXX&3 and did you try SWAPPING the coil from the variouse cylinders on the front to see if the codes change at all?