One of the most common mistakes beginner organists make is to keep the uneven tempo in their pieces.
Where it's easy, they speed up, where it's difficult, they slow down.
No matter how hard they try to keep the steady tempo - it's just too overwhelming.
Here's the trick which CONSTANTLY helps me to be precise in my playing:
In rhythmically difficult places I keep counting and subdividing the beats down to the smallest rhythmical value of the piece.
Let's say, you're playing BWV 554 and some places of this prelude and fugue in D minor are more difficult than others.
What beginner organists often do, they slow down in the middle of the fugue where the pedal part comes in. They do this towards the end when the texture gets more complex.
Since the smallest rhythmical unit here is the 16th notes I recommend counting in these note values.
In your mind keep a steady flow of sixteenths. Then you won't have to worry about uneven tempo.