I have a 99 5.4L F-150 Truck that has me mystified. It seems to run fine when it's cold, but after shutting down for a few minutes and then driving it while it's still warm, it runs rough and shudders. It seems to get worse over time. The engine light came on and and indicated misfires on two cylinders.

I replaced the plugs last weekend, and it seemed a little better for a while, but now it's back to the same problems. It almost seems like it's an overly lean mixture after it warms up...maybe caused by a bad O2 sensor? I've seen another post that mentioned the coils going bad. Any ideas on how to troubleshoot this?
Thanks!

 

Welcome to the forum.
Usually if it is lean, it will give a code for that. Since it is giving codes for specific cylinder misfires, It could be coils going bad. Which cylinders are showing a misfire? Any signs of heater hoses seeping into the plug pockets back around 3 and 4?
You can try cleaning tha MAF just to be sure.