Unfortunately, your save isn't going to be compatible with FoV:DKS. Basically with DKS, the format of the save file itself has been changed (there was a LOT of changes with DKS). Saves from the original Ego Draconis will work with the original Flames of Vengeance, but cannot be used with DKS at all (you cannot even open the save up in ED:DKS) and vice versa.
To give you an idea of how truly incompatible, a dev has already talked favorably about creating a patch that will take ED/FoV and convert it to DKS, but with the understanding that anyone that does this will have to start the game over. Even with a patch, the save games cannot be updated in any way. There just is so much changed content (revised quests, removed landmasses in the flying fortresses, etc, etc, etc) that not only will the patch not update the save games, it would also be impossible to attempt to do so.
My recommendation, as I've just played through for a second time myself after having the game for less than a month, create a new character and play a totally different class. If you played as the good guy, play as the bad guy this time. Possibly change what gender you played. It was a lot of fun seeing the different reactions from people, and even found that at times the rewards were drastically different as well.
