Sage,
When you go from Reverse to Drive, does your tranny take a good 1 1/2 to 2 seconds before you can press the accelerator? My 02 FX4 4x4 5.4L started out by having a delay from R to D, then it started "clunking" and slipping when stopping fairly quickly and trying to take off. I had the dealer check it out at about 8000 miles and the tech said that he could verify the problem but even after taking the tranny out and apart, he really couldn't tell what was wrong.
He did say that there was a seal or gasket in the area of the pump that was leaking internally and he replaced it. I have asked for a copy of the paperwork where the service was done and have yet to receive one. Needless to say, when I got my truck back, the problem was gone.
Ford has had some problems with the 4R70w tranny and yours may fall into one of the problems listed on alldata's web site.
Check out
http://www.alldata.com/TSB/20/012017DA.html
This is for the 2001's, but my truck had the delayed engagement issue and is now working.
Hope some of this helps.
Creole