The most important thing to remember here is this: you should practice slowly. No matter how boring it may sound, you simply have to have patience and practice at a tempo in which you can avoid making mistakes. If you make a mistake, very often (but not always) it means that the tempo is too fast.
Achieving a fast tempo and fluency is similar to lifting weights. If you try to lift a weight for which you are not ready, you will hurt yourself but if you say to yourself “OK, even though I am lifting only that much, this is my current level. I will stick to the plan, and see it through.” This is so true because it is generally believed that you should raise the resistance level by only 10 percent every week for safe exercise. In other words, if you can currently lift 50 pounds, you should add 5 pounds after one week of exercising with this weight. Then add another 10 percent after another week and so on.
The same thing is valid for organ playing. Even though you might think that you are progressing too slowly and you are not able to achieve the fast tempo yet, you are making progress, if only you are practicing correctly and slowly. You can even use the metronome for choosing the tempo. Just like with lifting weights or any kind of physical exercise, increase the speed of your metronome by 10 percent every week. When you are ready, the faster tempo will seem natural. Just have patience and you will succeed. In fact, very often people give up playing a certain organ piece only days before a real breakthrough.
Build up Your Technique
If you feel that achieving the fast tempo is too challenging, it might mean that you need to work on improving your organ technique. Try practicing daily exercises like scales (natural, harmonic, and melodic versions in both major and minor keys), and chromatic scales in parallel and contrary motion in octaves, thirds, tenths, and sixths over four octaves. Also play regular and long arpeggios and chords on a tonic, dominant, and diminished seventh chord. When these exercises become easy, later add scales and chromatic scales in double thirds, and sixths.
All of these exercises can be practiced either on the organ or on the piano. Take a pair of major and minor key with the same number of accidentals and practice all of the above scales, chords, and arpeggios for a week. Then every week practice different keys according to the circle of fifths. If you have very limited practice time, work on your technique at least for 30 minutes a day. After a few weeks you will start to see some real changes in your organ playing. A wonderful collection for improving your manual technique is Hanon: The Virtuoso Pianist which include all of the above scales, and arpeggios in part 2 and 3 plus many more exercises for finger dexterity, evenness, and strength. I recommend playing the exercises from Hanon: The Virtuoso Pianist before your regular organ practice because it also serves as a fantastic warm-up.
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.