He did around twelve, including the Toccata and Fugure in d minor, the Violin Partita in D - Chaconne, one of his best, the "Little" Fugue, "A Mighty Fortress," the E Major Preludium and "Komm Susser Tod" which is the best of all. He conducted all of them, though there is a new recording out by Pekonnen. Many of the recordings were in mono, done around the time of "Fantasia" though I have an LP that has the best of the transcriptions and performances and they are stereo. It is the one I mentioned before, that has been re-released on CD but the mix (re-mastered) is not as good as the old LP.
You're right about another level - that's what I've always thought about the transcription/conducting/performance/recording of Stokowski which are all among the best I've ever heard. Stokowski, having written the transcriptions, was able as an equally great conductor to get performances that are simply uncanny in their expressiveness. Also, he was very "hip" to technology and seriously approached recording while other conductors were looking down their noses at it.
By the way there is an interesting parallel to these transcriptions in film music - Max Steiner wrote a good score for the 40s Universal horror film "Beast with Five Fingers" that included a transcription, probably influenced by Stokowski, of the Chaconne as part of the score. It was not plagiarism but a clever integration of the music being played by a one-handed classical pianist.