The first exception to the rule of legato articulation concerns the repeated notes in organ composition. Whenever you see the repeated notes in the same voice they have to be performed in a very exact and precise manner. The repeated notes should be shortened by half of their value if the note could be divided in half (duple meter). For example, shorten the quarter notes by playing eight notes and have eight note rests. If the meter is triple, look at the music and decide what the shortest value is that you see most frequently in this composition. We will call this shortest value unit value. Shorten the repeated notes by unit value. For example, if the meter of the piece is 3/8 and the sixteenth notes are most commonly used, shorten the repeated notes by the sixteenth note.
The second important exception of the legato articulation is the staccato sign. The staccato literally means “short” and is indicated by the dots under the notes. The most precise way of performing the staccato notes in romantic and modern organ music is to shorten them by unit value. For example, if the staccato sign is given under the eighth notes, and the unit value of the piece is the sixteenth note, make these notes shorter by a sixteenth note rest. If the unit value is an eight note in such a piece, shorten the note by half.
Notes Before Unison
The third exception of the legato articulation is instance when one of the two voices is stationary and later these two voices form an interval of the unison. In other words, if there is a spot in your organ piece when one voice comes into unison with a stationary note, it is not possible to play the voice which was stationary legato. You should shorten this note by unit value. For example, imagine that the most frequent notes in the piece are the eighth notes. That is unit value. The top voice has two quarter notes D and D and a half note G. The lower voice has a two half notes G and G and the second G is in unison with the top voice. So the rule says that you should shorten the first G of the lower voice by unit value (an eighth note rest).
Try to locate above exceptions in your organ music and practice shortening notes exactly by unit value. This will give your performance the necessary precision, clarity, and vitality.
The above exeptions are discussed in great detail by Marcel Dupre in his 79 chorale preludes for organ which are fully edited, fingered, pedaled with complete registration and serve as a great introduction before playing Bach chorale preludes.
If you are interested in performing Romantic organ music, you might enjoy reading "Playing the Organ Works of Cesar Franck" (The Complete Organ No. 1) by Rollin Smith which I highly recommend.
By the way, do you want to learn to play the King of Instruments - the pipe organ? If so, download my FREE video guide: "How to Master Any Organ Composition" in which I will show you my EXACT steps, techniques, and methods that I use to practice, learn and master any piece of organ music.