Could you show us the place where you're seeing the trans numbers? I've never seen where you're talking about. But when they went from the Old Body Style to the Super Duty's, they went to a 4R100.
The compressor housing is stock. Not sure about the compressor wheel or turbine housing. The turbine housing will say what the A/R is.
As long as the EGT probe is before the turbo near the manifold, you're good.
Mileage probably won't be much different. Usually around 15-16 is a decent average.
I do my FF every 15k, more if I'm towing a lot and sending a lot of fuel through there.
Intake looks fine, that's how mine is. The stock air box is known for breaking and letting dirt in behind the filter.
As long as your trans isn't constantly hunting gears, run whatever you like. I keep my OD on unless I'll be running too slow and out of the power band for what weight I'm pulling.
And as long as you're not red-lining, you'll be fine. Never really heard of anything bad running high RPMs for a long time. Just watch your EGTs and trans temp of course.
If it starts longer hot, there may be an issue with the HEUI system.
How HEUI works and best to convert
Not to make you feel dumber, but read that
It's the best explanation I've found for how our trucks run the injectors.
So, once your oil is hot, it's thinner. Usually 6.0s have an issue with small High Pressure Oil system leaks and no/long starts when hot since the oil is thin. There might be a leak externally or internally. I'd try an oil change first if it's about time. Every 5k, maybe 6.5k max unless you do a UOA.