I copied this from my post to here so it would be more searchable in the future of other to find..

For anyone wanting to install OEM flares..

(Disclaimer) This worked for me and I don't know if all Ford OEM Flares have holes in the same place so take it apond yourself to make sure about the lay out before drilling....

*Parts needed*

OEM flares with clips and studs with nuts
(22) 1/4" tree push plugs
narrow and wide painters tape
5/16" drill bit, I used a stepped bit, but if too long will hit inner fender well on rear installs
1/4" drill bit
tape measure
10mm socket

*Install Steps*

1- remove all clips from flares, note the (2) 10mm studded clips at the bumper end of the front flares

2- remove tree push plugs, 1 front very bottom of wheel wells, 4 total, hold flare to truck if unsure which plug to remove, save these for use in step 5, but don't use for finial install, use new plugs only for finial install.

3- place narrow painters tape on the outside top edge of all flares, mark the center of all clip locations on this tape.

4- place wide painters tape on wheel wells covering about 5" to 6" including the inner lip...

5- position flare on wheel well opening, install the old plugs in bottom hole(s) (old plug are easy to remove, this is why you don't reuse plugs for finial install) have a buddy help hold the flare in position, flat on wheel well or tape in place if no one to hold them, Note t$ts on the flare to the line in body panels will also help line up the flare, hold or tape at the 4 point where tree plugs will go into inner wheel well lips.....

6- trace around flare edge onto painter tape on fenders, then transfer the center clip marks to painter tape on fenders also. then hold flare in place and mark the 4 tree push plug hole on inner lip.

7- remove flares off truck, remove tape off flares and reinstall all clips.

8- mark clip holes on truck 9/16" on center, down from trace line of flare,
this is for all clips except the front flares bottom stud closest to the front bumper, its 11/16" on center, just the bottoms, not the second stud above it, it will be 9/16", same as clips...

9- drill 5/16" holes for all clips and studs on wheel wells (48 holes), drill 1/4" hole for all tree push plugs on inner fender lips (16 holes)

10- remove all tape from truck and make sure to paint the edges of the drilled holes to keep from rusting..

11- install flares, drink beer, look at flares, drink beer, wash truck, drink beer..
after a job well done and a 6 pack, your heart will slow down from the 64 holes you just drilled in your truck..... mine did.... good luck...

 

That's the one thing that has kept me from doing this (along with having some difficulty finding AZ Beige flares that weren't straight from the dealer with the dealer pricetag). I think I'd almost rather take it somewhere and have it done. I'd be too worried that I would screw up and end up with 65 holes.

 

On one hand thanks a ton for the write up, on the other...CURSES haha. I just snagged a set of flares off ebay and now it's sinking in that I got to get the drill out and violate perfectly good fenders. :o Like most others I'm dreading the drilling process, but in the end I'm sure it'll work out and be worth it. I'll definitely have the beers on ice, but saving them til the drill is unplugged. Learned that lesson long ago

 

Most definitely have the drilling done before beer, thats why its in step 11