1. Relaxation. This is the most important point to remember. Although playing organs with a hard tracker action can create much tension on your body, you must learn to relax while practicing and performing. Deep regular conscious breathing helps your body to relax.
2. Use large shoulder muscles. When you encounter an instrument which keys are difficult to press, you should not work so much from your fingers which have a relatively short endurance span. Instead, use your deep shoulder muscles which will allow you to play for longer periods without tiring.
3. Play scales in double thirds and double sixths. It is a very wise idea to build up your technique in order to be physically fit. One of the best ways to develop the independence of your fingers is through regular practice of scales in double thirds (and even double sixths if your technique allows).
4. Practice with couplers. If you know that you will be playing a large mechanical instrument in the future, one of the effective ways to simulate the conditions on the organs that you usually practice is to engage mechanical couplers (if there are any). This way at least one of your keyboards will be more difficult to play and you will be able to get used to this touch ahead of time.
5. Take a slower tempo. When you play complicated instruments, it is always a good idea to reduce the performance tempo significantly. You don't need to play at the same tempo as you would on electronic instruments. Furthermore, very often such organs are located in buildings which have large reverberation so actually playing at a slower tempo significantly increases the clarity of your performance.
A word of caution: always listen to your body for best results. It is important that when you practice these strenuous exercises, you must rest before you are actually tired and before you feel the muscle fatigue coming in.
To feel some tension is OK but you should be always very careful of not to overexerting yourself. This way you will avoid muscle strain which can be dangerous to your arms and hands in the long run.
Use these tips in your organ practice today. If you consistently apply my advice in your practice, you will have no problems playing large organs with complicated key actions. Remember that you have to prepare for challenging conditions in advance so practice accordingly even on small practice organs.
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 free Organ Practice Guide.
Or if you want to learn to improvise in the style of Bach, I suggest you check out my free 9 day mini course in Keyboard Prelude Improvisation.