I have the same issue. Swapped a 85K 1.6 EB engine for a 25k engine, summer 2023. I had to replace the head due to plugs stripping. I optted for an engine replacement due to the "low" miles on the replacement engine. Note, I couldnt get a sales receipt for the engine purchase from the mechanic....
The engine has less power when under load (1% grade or greater, passing, maintaining 2-3 or greater on cruise.) Gas mileage is 7-8 mph down, on average. Its been tested and looked at numerous times by the mechanic and also by a Ford dealer. There are no codes and all say its normal and we cant reproduce the complaint. My 18 year old daughter even picked up on these issues immediately.
I have no ideas left. New plaugs were put in. Knock sensors changed being Ford somehow came up with a code for them. I was told the turbo was tested, called for vs actual turbo readings, and said there would be a code if it was off. All I can think of, is the existing turbo isnt performing as well as the prior turbo unit. I still have the previous turbo unit. There a lot of my time if I attempted to switch them just to test.
I am search for a needle from the haystack to make this car back to the way it was for her.