There is a fix for the 1-2 'bang shift' as it's been called here. This sounds a lot like what your describing when you accelerate and then brake quickly. Try a search for 'bang shift' which should provide the info you can take to the dealer for this low cost fix. (The TSS sensor was updated IIRC)
Links:
http://www.contour.org/ubbthreads/showflat.php?Cat=&Board=tranny&Number=257675&page=&view=&sb=5&o=&fpart=all&vc=1
http://fordparts.com/cart/?pn=+1S7Z-7M101-KA
The shift RPMs will be higher on hard accels and should reach up to and beyond 6250+ on WOT pulls. For normal cruising, 3500 does seem higher than normal, and may indicate a problem. This could be corrected by the bang shift fix mentioned above.
Changing the fluid 3x was a good idea as burnt fluid will only make any problems get worse faster.
