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I'm guessing your filter might be hitting the motor mount.
It may have the wrong filter on it. If I remember right, you should have the Motorcraft FL-820S, which is shorter than the Motorcraft FL-1A.
EDIT: I think the threads are different on the two filters I used in my example (metric vs. sae). They are just used as an example.
My parents '02 Explorer calls for one or the other, it takes the FL-820S but apparently it wasn't a for sure thing and there must have still been some FL-1A 4.0's floating around to still be in the book.
Did the 4.0's have the angle adaptor like the earlier engines? If so it might have rotated on the block...
My 2.8 had something like this from the factory so the filter pointed straight down:
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That is interesting that it would have two listed. I thought all of the OHV's were FL-1A, and the SOHC's were FL-820S's. I am pretty sure they are different threads.
OP, If it is rubbing on with the FL-820S, I believe the FL-500S will work as it is a little smaller. I actually remember hearing the aftermarket was going to drop the FL-820S size in favor of the FL-500S. So right now, Motorcraft is the only way you can get that size (or soon to be). The previous owner of my truck put a smaller aftermarket filter on my F150, and it is PUNY!