New truck--new problems
 

I just picked up a 2000 F150 5.4 Supercab 4x4 XL last week and I'm looking for advice...It has a random misfire issue throughout all RPM ranges. Did flash a code for me after driving for a while and I ended up replacing one of the COPs, which helped a little bit. Checked the rest of the COPs by disconnecting each while engine was running and listening for roughness. Cleaned the incredibly dirty K&N filter that came with it, and fixed two badly rotted vacuum hoses coming off of the exhaust manifold (EGR stuff I'm guessing?)

Still ran a little rough, and I ran out of time to work on it over the weekend so I took it by Precision Tune to have it diagnosed. They found water in the cylinders (not coolant, just water, possibly from the detailing before I bought it.) So $300 later, the water is out of the cylinders and they coated everything with dialectric grease, but not much more improvement. Compression test was good, except one cylinder was lower than the others @ 145, but they said it was still within spec.

What to check now? Is the lower compression something to worry about? I'm planning on changing the spark plugs this weekend with some Motorcraft ones from the dealer. Should I try a fuel filter too? 02 Sensor? I really want to avoid just throwing parts at it and I'm new to the mod motors, so any troubleshooting tips would be appreciated.

your on track so far. thoes two vacuum hoses on the EGR system do get hard and crack. The K&N filter is not helping. It might be letting oil get thru to electrical components down stream. Spark plugs is a good idea. Water around the plug and coil will short out and cause problems as you said. You may still have a bad coil that is not giving a code yet. You might want to consider buying a hand full of coils as replacements as time goes on.. you can get a full set on e-bay for about $100.

Will check into the complete coil set...just got the plugs, so I'm still waiting to install those and see if it helps.

Ditto on the filter and new coils. Might want to put a motorcraft filter in and clean the maf sensor.