Not sure why there should be duplicate textures. The variations should be listed by manufacturer & variation in alphabetical order just as in FS2002/4. These are the Aircraft.cfg ui_manufacturer & ui_variation entries.
Quote:The first line of the texture listed a Paint No. Does the Paint # have to coincide with the fltsim number?
Not seen this entry but I don't have the full version of FSX. In previous versions of FS (including the FSX Demo) the title= name of the defaults is usually numbered as Paint1, Paint2 etc. which match the [fltsim.x] & texture folder names for convenience. These entries can be anything you like providing they're different to all other variations of the aircraft.