Hello GreenRoomSon,
Last Nov. 2023 I purchased a 17 XLT with 164K. I purchased from a used car dealer and I did buy the offered extended warranty (24K miles/24 months). I did a fair amount of research on the 3.5 Eco, have been a lurker for a long time. Coming from an 09 F150 SuperCrew with 5.4 and same 6 spd transmission. I'm not sure about any particular issues with the 6spd transmission beyond early versions which had some PCM/transmission module programming causing erratic shifting in certain scenarios. I had zero issues with my 6spd transmission on my 2 F150 2001 and 2009.
In addition to the Cam Phaser issue, which Ford redesigned, there is a vacuum pump bolted on the rear of the right side head (drive by the cam). The vacuum pump is known to leak oil and eventually produce insufficient vacuum causing various error codes and performance issues. The exhaust manifold issue is similar to the 5.4 manifold issues however on the 3.5 for neglected to use several available bold holes.
DB Diesel offers upgraded replacement manifold (as well as Turbos) for the 3.5.
My 2017 Expy XLT did have a bad main (larger) turbo, and exhaust manifold which made a high pitched screeching sound under heavy acceleration. I thought the noise was coming from the passenger side (small) turbo. After having my local Ford dealership, litterally around the block from my house, perform a "Works" package (oil change and a several dozen point "inspection" they informed me the screeching was from the manifold, and a failing water pump. They also cited the vacuum pump as the source of an oil leak/drip. I took it to a reputable local independent shop and they determined: Large turbo was bad, passenger side manifold was leaking, and the vacuum pump oil leak/drip was from the timing cover, possibly caused by the used dealer when they replaced the water pump.
While the timing cover was off to address the oil leak, I had them check the timing chain and cam phasers, they replaced all and ensured the cam phasers were the new design. They also installed the DB Diesel manifolds (both sides) and the large turbo. The mechanic said the cam phaser adjuster was extended to the max and only a mater of time until the ECU/PCM started to throw timing codes due to the chain being stretched.
Thank fully the Warranty cover the Large Turbo and the labor for the timing cover, so that softened the blow. Just some things to consider. I am playing the long game on this Expy and didn't want to wait for the timing errors which would have provided the warranty coverage for the chain. My luck is that issue would have started 1 day after the warranty expired. Murphy's Law seems to by my shadow, always lurking around.
Cam Phasers, Timing chains (at higher mileage) and Manifolds are the real mechanical issues to be aware of. I expect to run this truck to 300K.... Hoping anyway.
Best of luck.