5.4 with a misfire that I cannot explain. Who is an engine wizard?

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I have a 2004 F150 with the 5.4L I replaced the factory muffler with a Flowmaster, installed an AEM Brute Force Cool Air Intake, and an Edge programmer that has been upgraded by Power Hungry Performance. The truck has 95k on it and I got it with 12k. The Edge, AEM, and Flowmaster have been on it since 30k. Didn't get the Edge changed to a PHP until 80k.

Ok, now the issues. I have randomly had lean codes with this setup but only when it is VERY cold outside. Once the engine warms up it would go away; started after I put the intake on it. Maybe get a lean bank 1 & 2 twice during an entire Nebraska winter.

Since about 60k my engine has had a bit of a diesel sound to it. Thought it was the cam servo issue but mine seems much louder. At around 75k it started to develop a miss. It seemed to only happen when under a high load (low RPM going up a hill, that kind of thing). The miss got worse and worse to the point I couldn't even set the cruise when driving down the interstate. The truck would shake and sputter. It even would sometimes miss just idling at a stop light. Thought I might have a plug issue. Put in new plugs and did a full intake cleaning at the dealership. Issue came back after a month. I replaced all 8 coil packs thinking it might be one of them. No progress made with this change. Had the plugs changed again. Tech said the month old plugs looked like they had 80k on them. Said they looked burnt.

I checked to see if the programmer was the issue; even with the truck tuned to stock; still have an issue. Had them smoke the intake to see if it was sealed up tight, they said it looked good. And to make matters worse, the tech that worked on the truck said that the miss what happening in random cylinders. Not just the same one. Replaced the fuel filter. Checked the fuel rail pressure. Everything looks good. Ran a can or 44k thought it... Still has the same issue and still no ideas.

So who out there has some ideas of what it could be? I'm starting to think that there are some valve train issues.

Anyone have any ideas?????