I never noticed the window speed. You will have to take it in to have the door handles fixed on warranty (recall). As far as the transmission reflash goes, good luck, see the transmission problems thread.
The transmission is a weak point and seems to problem prone.
At least the 07 engine and drive train (except transmission) brakes, steering and all seems to be working OK at 5600 miles.
No rattles, shakes or other wind noise. (yet)
The passenger door Expedition badge is falling off.
I had to paint the guage red indicators white, so I can see them in the day.
The front licence plate bracket will fall off unless you use some big long sheet metal screws to hold it on with.
The heating and cooling controls work, but have a mind of their own at times and will turn on the AC compressor in very cold weather if you don't watch it real close.

All and all I would say that my EB 4X4 07 is "OK" but that's about it.
A few good points: Great sound system.
A lot of power.
Would I buy another one?
Don't know.
I would read all these posts to get an idea what to look out for and there are some good people here that can help on those difficult problems. Everyone here has really helped me out a lot already.