One of the most important things if you want to learn pieces faster is to practice them in a slow tempo. Generally, you have to use the tempo that is about 50% slower than the concert tempo. This will give you accuracy and help avoid making mistakes.
Before learning the piece, try to write in fingering and pedaling. Remember that it is not required to indicate every finger and pedal in the entire piece right away. Instead, you can write in your pedaling and fingering only in the episode that you are working and practicing.
Another thing to remember is to practice in fragments. This will help you to correct any mistakes easily. When you practice your piece, play separate voices repeatedly so that you can master them individually. Only after that work on voice combinations such as two parts and three parts together. After this becomes easy, try to play all parts together over and over.
One more thing to remember when you practice these episodes is to aim for correct rhythms, notes, ornaments, articulation and hand and feet position with every repetition. Do not proceed to the next step unless you can play it fluently at least three times in a row.
Above all, try to practice every day. Not necessarilly for several hours, but at least for 20-30 minutes. Even if you have that little time, you can still make progress - you can repeat previously mastered material instead of learning something new (which you can do on days when you have more time to practice).
Organ practice can be compared to boiling water - the minute we take the pot off the fire - the water begins to cool down. So if you want your organ practice to be in a good shape - do it every day.
Also don't neglect the importance of having an exact measurable goal and a plan of action to achieve this goal. This will definitely speed up your learning process. Otherwise, your playing might be just wandering around in circles.
If you really want to learn organ pieces faster, then you should perfect your organ sight-reading and harmony skills very systematically in a step-by-step fashion. This is how I'm able to play 12 recitals a year with different repertoire.
Consider these recommendations when you take your organ pieces and apply these tips in your practice. Finally, you have to be very persistent in your practice and then you will succeed in learning organ pieces faster.