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I had a set on my old F-100, but they were on when I bought it and I couldn't tell you if any mods were made or not.
My current truck is an F-100 2wd on a '78 F-250 4wd frame and the crossmember was notched out with a torch / grinder to get clearance for the driver's side collector.
I'm sure somebody will chime in with better info for you.
I put Hooker Super Comps on my '66 F100 2WD LWB 352. They are not ceramic coated. They were a bit of a fiddle to install, especially on the passenger side with having to remove the starter among other things, but the directions were spot on. I then had a local muffler shop custom make the rest of the system. It did not hit the crossmember. I should add that this was all part of a complete rebuild with new cab mount and core support donuts. The only issue I had was when I decided to change transmissions and the "H" pipe was routed right under it. Had to have the muffler shop make the "H" pipe double flanged so it could be removed.
Sanderson makes a set that were designed for the FE in 61-66 F-100s... They are shorties that collect and drop straight down between #2-3 AND #6-7 Cylinders. They are short enough to ad your exhaust pipe and run it back WITHOUT the problem of roasting your starter. Also makes it easy to remove your starter. I remember a guy that also made a short section of the exhaust that can be removed very easy should you want more room to remove the starter. The short piece of removeable exhaust was from the collector to just past the crossmember support. He also said it wan't really necessary to remove that piece of pipe but it was there just in case.
The Sandersons are however not cheap... BUT a good set of perfect fit headers will last a very long time. Sanderson does NOT want you to use exhaust gaskets but rather their RTV type sealer ONLY.
Fritz
I had my duals put on today. For now Im keeping the stock manifolds. I have a good FE block and 390 crank to rebuild if the 352 craps out. I really would rather go with a 351/AOD next, so I didnt want to spend $400 on FE headers until I decide.