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I just picked up a 2001 F250 SD with the 5.4. I also have a 1999 that is nearly identical (minus the 2001 having A/C)
Something strange I noticed is the the shift lever in the 2001, in Park, is damn near up against the dash, less than a finger length away, The lever on the '99 is right where you'd expect it to be.
The indicators in both trucks are lined up properly, but I'm rubbing my knuckles every time I shift the '01 into or out of Park. Is there any other adjustment? Nothing seems to be bent, and neither steering column is adjustable.
1999:
2001:
You can see in the photos how much closer it rests. There's also much more play in the '01. In the '99, I can pull the shift lever straight back about 2" from its resting position. The '01 can be pulled over 3-1/2" Not sure if that really means anything.