You see, a lot of this to me is simple mathematics. Some parts of the piece are easier than the others. For example, if the fugue starts with just one voice without pedals, this will naturally be much easier to play.
If you can play one voice smoothly and without interruptions after just several careful repetitions, it doesn't mean you will have the same success when you have 4 voices with pedals.
Adding one more voice add just one more constrain to your practice. It is like just one step further. Especially having pedal part in you score can complicate things because naturally you are much better with your hands than you are with your feet.
You have to be ready for the next step. For example, if you take 3 voice combination without mastering 2 voices and separate voices first, then the success will not be as great as it might be.
My advice is not to advance to the next combination unless you can play the current one fluently and without interruptions at least 3 times in a row correctly (with correct fingering, pedaling, notes, rhythms, articulation, and ornamentation).
So you see how in reality there is no need to be frustrated about slow progress. You have to understand that there are no shortcuts in organ playing. If you want the fastest possible progress, just stick to the systematic practice method when you learn by voice, by two voices, by three voices, and by four voices one short fragment at a time in a slow tempo.
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 really want to learn to play any organ composition at sight fluently and without mistakes while working only 15 minutes a day, check out my systematic master course in Organ Sight-Reading.