I have an 08 F150 5.4 4-speed auto 4x4 with 3.55 gears and 135k miles on it. A while back it started making a "skip" from somewhere in the drivetrain in which the engine wasn't hiccupping but it felt something like if a chain and sprocket or a mechanical gear was skipping a tooth kind of thud. It has gotten worse lately and I'm trying to figure out what it is as it only does this in Overdrive at low RPM and usually only going up a grade. Rear end fluid was changed 40k ago, tranny fluid 20k ago, transfer case and front end fluid less than 1k ago and there were no shavings in any of the fluid changes. The truck also has 33" tires and a 2.5" lift. Any help would be appreciated.

 

I'll bet you good money it's your ignition coils. I have a 2007 Lariat 5.4 Triton. I was having problems with mine and I thought it was my tranny. It sounds a lot like what you're describing. Finally I threw a code and it was a coil. I replaced that one then another one went. I ended up replacing all my coils and the spark plugs to boot. That was over a year ago now and my truck is running like a champ.

 

https://www.f150forum.com/f4/tranny-issue-448094/

 

most times this comes up it is an ignition misfire. Change plugs and boots first.