I can understand this perfectly well. You see, a lot of people who are new to the Baroque articulation of organ music (not necessarily new to the organ playing in general, but just new to this style of articulation) spend their all energy focusing on the articulating the hand parts.
What often happens is that they forget about their feet. It's difficult to think about several things at once and since on the organ we are constantly multi-tasking, some tasks might be left unchecked.
If you found yourself in this situation, my strongest recommendation is to practice the pedal line separately until you can make small spaces between each and every note. Mentally think "note-rest-note-rest-note-rest" and so on.
Then practice soprano and bass, later - alto and bass, and finally - tenor with the bass together. The next step would be to play soprano, alto, and bass, later - soprano, tenor, and bass, and alto, tenor, bass. If you do all the previous combinations, then playing all four parts together with the right articulation in the pedals will be very easy.
By doing so, your ears will become gradually accustomed to listening if the pedals have the perfect articulation - articulate legato.
Note that we are not talking about learning this piece from scratch. Instead, we are trying to find a solution to fix the articulation problem in the pedal line. If you are new to this piece, there are of course other learning methods to follow.
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To your success in Bach organ playing,