When they put my bedliner in they used the factory screws, they were plenty long enough. Don't know why someone would change the screws unless the tailgate liner is alot thicker than the ones I've seen.
They make two different screws for the tailgate, one with a shoulder on it
for the liner and one without the shoulder to use without the liner.
I changed mine when I took the liner off also. If I still have the Ford part
number for them I'll post it here.
A word of caution...When you install new screws don't use a power tool.Use a drop or two of blue loctite and don't tighten very tight.I have seen what dealers do to the screw holes and it isn't pretty.
Sorry guys, I should have stated I took OFF the dealer installed drop in liner. I think JHEMR has it correct, I need new, shorter screws.
Found the Ford part number for the bolts "N806149 S301"
The liner on the tailgate is held on with 8 longer bolts that have
a short unthreaded section (shoulder) up by the head, these also
help hold on the access cover on the inside of the tailgate, there are 10
screws total that hold this cover on. The part number above will match
the two that are under the liner. This is what I did to mine and yes I
went to Ford to get the screws, they were about 80¢ each, but they
all match and you can't tell there was ever a liner on the tailgate.
Hope this helps.... Joe