I bought my truck last September. The build date is 08/03. Since then I've been reading a list of problems that some have had. I've been recluctant to post any of my problems due to hoping mine would play out as I broke the truck in. Anyway here is what I have as far as know. The truck has 9200 miles so it has had ample time to settle in. It is a 5.4l, 4x4 supercab.
1. Clunk sound when taking off, sometimes
2. Bed bounces
3. Little rubbing sound when turning
4. Rear end shudder around the 75mph
5. Throttle response delay

The clunking sound was so intermittent that I did not really worry about it untill this Friday. On the way to lunch a lound "CLUNK" was heard. Seemed to have came from the transmission but who know's. I read a post by PC Poppy and he found out that
"They removed the driveshaft and lubricated the splines on the yoke with silicone grease, where it goes into the tranny. This must slide smoothly back and forth under torque. " So I'm taking it in this week to have it checked out. While I'm there I'm going to have them check out the rest of my little bugs. I know about how the throttle response work but mine seems to be particularly. Anyway I am not trashing Ford or my truck. I love my truck and have been in "denial" about my problems. Hence me not taking it in for every little squeek. I'll keep you posted on what my local dealer has to say.