The reason you should take aside some time regularly for ear training is not only because then you will develop perfect pitch but also become a more complete musician. Then you will be able not only to perform your organ music but also understand how the piece is put together which will enhance greatly your and your listener's appreciation of the pieces your play.
However, it is not easy to recognize intervals, modes, or chords, if you are not following step-by-step systematic approach. Many people simply get overwhelmed, frustrated, and quit their ear training because of that and even start to question whether or not this skill is practical and useful. So it is even more important to overcome these obstacles and here is how to do it in 4 simple steps.
1) Play. The first step to take is to play these musical elements on the keyboard. Simply choose a scale, an interval, or a chord and play it from any of the 7 diatonic notes and later from the 5 chromatic notes.
2) Listen. After playing becomes easy, ask somebody to play the elements for you and try to recognize them. In order to make this step easier you could also record yourself playing scales, intervals, and chords from Step 1 and play them back using any device you have at hand.
3) Write. If you feel that you can recognize these elements most of the time correctly, try to write them yourself on a stave with pencil. Again, follow the order from Step 1 - first write from diatonic notes and later from chromatic notes.
4) Sing. The last step in mastering scales, intervals, and chords is to simply sing them. Now that you have done the previous 3 steps, singing should be just a little more difficult. Be very systematic about it and don't stop the exercise until you can do it at least 3 times in a row correctly and in tune.
By the way, do you want to learn my special powerful techniques which help me to master any piece of organ music up to 10 times faster? If so, download my Organ Practice Guide.