Let me start by saying that scales provide the benefit of finger dexterity. There is no question about that. In fact, that's the very reason why scale practice was invented in the first place. However, my experience in organ teaching and performance tells me that there are other technical exercises and etudes that are even more beneficial than simple scales.
If you want to reap more benefits, practice not simple scales, but scales in double thirds and double sixths (if your technique allows). As with all things, slow practice is the best. Fast tempo will be achieved naturally once you are ready.
Take C major and A minor scale and practice them by playing thirds in each hand. Next week take another pair of keys progressing in ascending order of accidentals (1 sharp, 1 flat, 2 sharps, 2 flats etc.). Try to play each scale correctly at least 3 times in a row.
Double thirds (and double sixths) are an integral part of any advanced organ music, so if you are serious about your organ practice, you should practice such scales repeatedly and regularly.
If you haven't done this kind of practice before, at first it will be quite a challenge just to play with correct fingerings even in a really slow tempo. Do not expect the results overnight. But if you continue to practice this way, your finger independence and technique will skyrocket.
A word of caution: since this is an advanced technique, be careful of not to overextend yourself to avoid any damage to your fingers and hands. Always be conscious of how you feel. Some minimal tension is fine, but as soon as your fingers and hands feel tired, take some time to rest and shake off the excess tension.
Scales are also good for giving the benefit of knowledge of circle of fifths, all keys and some music theory issues. So we can't really completely dismiss playing scales. But if you specifically want to improve your finger technique, try scales in double thirds (with correct fingering, of course).
On the other hand, pedal scales and arpeggios are wonderful in developing the flexibility of an ankle which is the key to the perfect pedal technique. As with manual scales, take 2 keys per week and master them.
Use the above tips when you practice scales on the manuals or on the pedals. They will help you to perfect your organ playing skills.
By the way, do you want to learn my special techniques which help me to master any piece of organ music up to 10 times faster? If so, download my FREE video guide "How to Master Any Organ Composition": http://www.organduo.lt/organ-tutorial.html
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