Too weird. I've just dowloaded the DOEConvert2.zip file to verify, and sure enough those files do exist in the download. They are also instructed to be copied in the ToEagle script. Since those are the only files you have missing, and all the files you do have follow the same command, it makes no sense that you aren't getting those 7 files.
In any event, since you downloaded DOEConvert2.zip, you do have the files you need. You'll just have to move them yourself. Just go into:
C:/Program Files/Taldren/Starfleet Command II/EagleConvert
and copy these 7 files. Once you've copied them, paste them into:
C:/Program Files/Taldren/Starfleet Command II/Asset/Scripts
That should get you in. If you didn't install SFC2 on your C drive, just subsitute the letter of the drive you did use above.
-Herr Burt