I was doing some research for a local club member and came across Baumann Engineering. They have a very comprehensive discussion about AOD vs. AOD E and also go through enhancements, ratios (stock vs FMS), important upgrades for durability, etc. The guide is found at
http://www.baumannengineering.com/pguide.htm and the home page is baumannengieering.com.
If you do look for a late '80s transmission, note that the Lincoln unit is almost 2 inches longer than the Mustang GT version. You may want to post for Parts Wanted on CobraForum in the event that someone wants to get rid of their donor car transmission. Pay special attention to the PV cable setup.
Hope this helps,
Gary