Part 1:

While Im sure there are a million threads for codes on here I wanna try and narrow down the problem and be specific

My wife was driving her truck yesterday and said the MIL light started to flash and the truck felt like "it was about to blow up" . So when I got home I busted out the trusty old scanner and this is what I got:
P0305- Cyl 5 misfire'
P0354- Ignition coil D primary/ Secondary circuit malfunction
P0304- Cylinbder 4 misfire

The truck is a 2005 5.4 with ~130,000 on it and it runs very well for the most part. I have done the spark plugs before the summer and replaced them with the motorcrasft sp-515s. Im guessing the problem will be with the #4&5 coil packs. is there a way to troubleshoot these?

Part 2:

So without troubleshooting further I just went ahead and changed the number 4&5 COPs. Truck seemed to be running well, until we just took a 2 hour trip up to the airport. Truck started to shake again and MIL came back on, I had brought the scanner with me and attached a picture of the new codes. Additionally I noticed the the truck has a stutter or hesitation on the highway at mid-throttle letting off or giving a little more pedal will smooth it back out.

 

Check for vacuum leaks. Run a couple bottles of Techron through the gas, you may have dirty fuel injectors. The 2005 5.4 did have a bad batch of injectors from the factory, but they usually leak or stick open giving you rich codes.

Wouldn't hurt to pull the #4 and #5 plugs and look at them.