Misfires have me beat
 

Hi all, new to the forum here and I am in need of some serious advice. I've got a 2004 F-150 with the 5.4l engine in it, and 166,000 miles. It suddenly started running really rough with some obvious misfires that seem to ease up quite a bit when I give it some throttle. At first I got P0306. Clear and reset. Then P0316 and P0305. I recently had all plugs and coils replaced, along with a new PCM so I took it into the mechanic who has done all of the work, assuming he would just replace some faulty parts under his repair warranty. Yesterday, I get a call from him and he tells me he truly can't figure anything out on it, and it is now showing P0316, P0301, P0305 and P0306. He has tried new plugs, and new COPs, checked for vacuum leaks, checked the PCM, inspected all the wire connections, and taken a fuel sample which came back okay. No changes. I told him that if he has ruled out anything under his own repair warranty, I will be limping it home (about a mile) and digging into it in my free time. So I have the truck back, and the strange thing is that I don't get any codes suggesting that I have a timing issue, and no codes suggest an injector issue... it all points towards the ignition system, which has been thoroughly combed over. Here is what I am thinking of doing, in this order, until I hopefully find the problem.

1. Inspect wire harness for damage, especially where it passes under the AC line by the PCM.
2. Remove intake manifold to see if coolant is leaking into the plug holes towards the front of the engine (cyls 1, 5, 6).
3. Compression/Leak down tests.
4. Check fuel pressure.
5. Pull valve covers to inspect camshafts and valves.
6. Pull timing cover to inspect timing components.
7. Give up and take it to the dealer.

I have looked all over the Google, and haven't really found anything useful for my situation. Has anyone experienced something like this? What would you look at first? Also, as sort of a side note, what results from compression and leakdown tests should tell me to start taking everything apart and preparing to drop a new engine in? Like, what mechanical damage to the engine is worth trying to repair vs just putting a whole new engine in? I'm pretty confident in doing repairs, but the troubleshooting is what is killing me.