Thanks for the Tip, Taltamir! My experience was similar to yours (as to the location of the extra directory files). Also, I found, not 1, but 3 files in: <user>/My Documents/My Games/Fallen Enchantress
that were appropriate to manually remove. They were a (seemingly) general Fallen Enchantress file, a Beta2 type file, and a Beta 5 type file. I believe that has left me with a Clean Slate!
(I think that many users may have slightly different experiences, based upon their specific Operating Systems, whether or not they downloaded Mods, and various other vagaries of their computers and/or their regular practices.)
Update: Just to provide one Beta tester's Download experience with v 1.00.0 . After de-installing the Beta(s), and starting with a clean slate, it took about 2 hours and 20 minutes to complete the download. I started a little before 3PM Eastern time, and finished a little after 5PM Eastern time. (I know that some folks claimed download times well under an hour -- Lucky them ! -- but on my (admittedly) not very robust InterNet connection, it took quite a bit longer.) The program is 3.48 Gigabytes. I was downloading initially at the rate of just over 800 KB per second, but the rate gradually slowed to about 450 KB per second. I don't know if this slowdown was due to more users accessing the Stardock server as the afternoon dragged on, or if my computer was just getting tired, and slowing down as a result. 
After the download, installation and configuration took perhaps another 20 minutes.
On the Plus Side, after this joyful passage of some 2 hours and 40 minutes, Fallen Enchantress fired right up, and appears to be working beautifully. 
I do think it is possible that folks who wait a day or two may find the whole process to be significantly faster/easier, after the initial rush of some 80,000 rabid Beta testers and Early Purchasers has subsided. Good Luck, All !
