I must confess to having very mixed feelings about this puzzle. I liked the ambiguity and its resolution, and the discovery of more than the minimum thematic material in the grid. However,I would have been happier if that hadn't been preceded by such a tough, and at times fiddly, workout.
The disordered clues was perfectly justified, but I couldn't see any justification for withholding answer or entry lengths. These wouldn't have given anything away since the clues were not i grid order. If answer lengths had been given that would have narrowed the options for the entry with two letters but that would hardly be much of a giveaway. Nor could I see the need for the instructions to be given twice, and as noted above, two extra letters in wordplay made things especially tough. It seemed to me that this was all done to make the puzzle more difficult without having much of a thematic justification (merely a double in the theme).
Other difficulties include ambiguities in the letter pairs in some clues, as noted by Hagen, and several instances where the two extra letters came from a three-letter abbreviation or word. Sorry, but that is just inelegant cluing.