My 1998 5.4 has started vibrating a little when you are at a stop with it in gear. It doesn't seem to do it when you are not in gear. The vibration pulsates. I had an O2 sensor problem that I thought was causing it. After fixing the O2 sensor issue, the vibration is still there, but not as harsh. There is no noticeable miss and I haven't had the check engine light come on. I have 93,000 miles on it and I have yet to change plugs. Any ideas? Or, should I change the plugs and see what happens?

 

It is probably due for a plug change.
My 2001 has had a slight miss/shudder since I got it. It seems to be normal in these things

 

Take a look at your vacuum harness that runs from the p.c.v to the back of the intake. it leaks at the elbow and at the back with about your milage.

 

Mine gave up the ghost at 35,000 miles. They replaced the whole PCV assembly under warranty. The MAF failed at about the same time.