I recently bought a 2003 F250 with the 6.0L. I decided soon after buying it to change the fuel filters, oil, and oil filter. I went to autozone and bought motorcraft oil and non-motorcraft filters.
After seeing the Ford powerpoint on why to never use non motorcraft filters in a 6.0L, I decided to order the motorcraft filters and swap them in after about 1000 miles on the autozone filters.
Below is a picture of the autozone filter I pulled out after only 1000 miles. It looks to me like it collapsed and was probably restricting the fuel flow. I had a 3 MPG drop in fuel economy on my last tank, and I drive a fairly consistent number of highway vs city miles (I drive 50 miles to work each way, mostly highway).
Its seems my acceleration is also better after installing the motorcraft filters, but it may be in my head.