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I was looking under the hood last night on my 08 250 with the 5.4 and found the main wiring harness on the drivers' side was rubbing on the upper front shock absorber bolt and had almost worn through the insulation right by the 'y' where the harness splits. It is held there by a plastic piece that secures the harness to a bracket, but that piece also pushes it against the shock bolt so check your sh.. and see if this is a common problem or is it just on my truck. Glad I caught that, it could have caused all kinds of problems a few weeks down the road, sometimes those failures can be hard to trace down.
I checked the driver's side shock bolt location you mentioned on my 2010 SuperDuty. I saw what you are talking about on how close it is. I did notice on my truck they installed a rubber boot on the bolt from the shock, preventing any chafting.
I had replaced my shocks with kyb's so maybe the studs are a little taller, but not by much though. Should still be an area of concern though for others to check.