When importing IE Favorites into Firefox Bookmarks, the IE Favorites are imported but without the custom sort order I originally had in IE. How can I import the sort order? (maybe editing some registry line?) I have too many Favorites to sort them manually. Thanks.

in FireFox

Import them.

Then click Bookmarks > Organize Bookmarks.

Thats all I can think of

Yes, you can click Bookmarks/Organize Bookmarks, but that's the manual method. Imagine rearranging hundreds of favorites this way, there must be a way of copying the registry key of IE that holds the sort order so to apply it to Firefox, which is:
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\MenuOrder\Favorites