You might try combining some of the episodes from the Special Edition so they match the Aired Version. Then use the aired order naming & organization when you put the files into Plex.
Aired Episode 1 = Special Edition Episodes 1 + 2
Aired Episode 2 = Special Edition Episode 3
etc.
Aired Episode 6 = Special Edition Episode 7
Aired Episode 7 = Special Edition Episodes 8 + 9
Special Edition episode 10, One Year Later, is listed as a Season 00 special in the Aired Order in TheTVDB.com.
See [HowTo]: joining multi-part movies files with MKVtoolnix GUI for info on joining media files together.
From Wikipedia:
Aired Order:
Episode 1: Preparation
Episode 2: London to Volgograd
Episode 3: Kazakhstan
Episode 4: Barnaul to Western Mongolia
Episode 5: Western Mongolia to Yakutsk
Episode 6: Yakutsk to Magadan (the Road of Bones)
Episode 7: Anchorage to New York
Special Edition
Episode 1: Preparation, part 1
Episode 2: Shoving Off
Episode 3: London to Volgograd
Episode 4: Kazakhstan
Episode 5: Barnaul to Western Mongolia
Episode 6: Western Mongolia to Yakutsk
Episode 7: Yakutsk to Magadan (The Road of Bones)
Episode 8: Anchorage to Calgary
Episode 9: Calgary to New York
Episode 10: One Year Later
