I know its not an answer you want to hear, but the problem with a question like this on a forum is there are way too many variables and possible causes to even begin to make a wild guess without having more information. Misfires on an engine like the 5.4 could be anything from fuel delivery, ranging from the common module corrosion to injector problems or fuel pump... could be an intake, or even exhaust leak or plugged CATS, plug or coil problems, could even be the PCM itself.... valve problems, head leak, Timing component failure... or a combination of multiple things.... the list goes on... so there has to be some diagnosing done to even know where to start.
It really sucks to have to pay a mechanic to tell you what "could be wrong with it"... but unless you have the time and ability to diagnose it yourself, that might be your best bet.
If you can gather some diagnostic info to offer, then hopefully someone on here will analyze it and have some insight.
I am in a related scenario, and recently posted a ridiculous amount of information,... thus far it seems any actual professionals highly knowledgable in diagnosing are probably too busy fixing everyone elses problems at work to read forums and help people out for free. LoL
its a bit lengthy but You can read my post
HERE if youd like an idea of various things to test for.