If this is the situation you are currently in, I feel your pain.
If you are hoping that these difficult pedal passages will get better on their own, you are hoping in vain. Or if you think that this complex imitative texture in the fugue will get any easier with time, think again.
Maybe that works for people who only enjoy playing the pieces that they love. For a serious organist, this is not good enough. But even if you only want to be able to play the composition, wouldn‘t it be more enjoyable to be able to play it well? How would it feel for you to achieve the level of competence when you can play the piece you love with precision, clarity, and ease?
Here is a thought: Always have a goal for your practice. It might be very small one (in fact, it‘s usually best to have a definite, precise, and measurable goal). Then think if each repetition of the piece gets you closer to the goal or away from it?
Now that would improve results of your practice, wouldn‘t it?
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 video Organ Practice Guide.