Whenever I play this or a similar free composition (not based on pre-existing material), I tend to use Organo Pleno registration. This basically means a principal chorus: in the manual, I play with principals 8‘, 4‘, 2 2/3‘, 2‘, etc. – all the way up until mixtures.
Often there is more than one mixture stop on some large instruments. In this case, I would probably use both of them (the low and the high one). If the mixture is really low (based on 4‘), it is best to add a 16‘ principal to the manual part. In other cases, 16‘ stop adds more gravity to the sound but is optional.
If I play this piece on the large organ, I usually also couple one more manual which has a bright sound (preferably not a Swell division). In this case, I might also build a principal chorus on this manual, if available.
If this particular instrument has narrow-scaled principals and high-pitched mixtures, such as in the Neo-Baroque organs, I might add 8‘ and 4‘ flutes to the manual part. Such trick usually adds gravity to the sound.
Sometimes the fugue sounds nice with a Trompete 8‘ which might be a good option on many instruments to add to the principal chorus. 16‘ Trompete in the manual part might be a little too thick. However, this is my personal preference only.
Although the organs of the Bach time in Central Germany usually had mixtures which included the tierce pipes, some organists add a 1 3/5‘ stop to the manual part. However, the result might be a little too harsh so you have to use your ears carefully.
For the pedal part, I would also use principals 16‘, 8‘, 4‘ (if available), and mixtures. 32‘ flue stop (Principal or Subbass) works for tis particular prelude and fugue quite well, so I might also choose to have it. When using reeds in the pedal, the first reed to add is Posaune 16‘ and only then Trompete 8‘ (if necessary). 4‘ Clairons don‘t work in this music, so I would save them for other compositions.
If the pedal part needs more power when compared to the manual sound, I would add manual to pedal coupler. However, there is a tendency to overdue this, so this option should be used with some consideration.
Keep these points in mind when registering Bach‘s free works such as preludes, fugues, fantasias, and toccatas. However, you should always look at the instrument before deciding if it is going to work for a certain composition. Look not only at the number of manuals, manual and pedal compass but also at the style of the organ.
If you are also playing chorale preludes of Bach, I also recommend you read about the ways you can register his organ chorale preludes.
Although it is said that Bach‘s organ works sound well on any type of instrument, I would probably not play them on a genuine Romantic style organ (with some exceptions, of course). Instead, I would choose to perform Romantic and Modern music on it and save Bach‘s pieces for another instrument.
If you have a large instrument at your disposal, often you might be tempted to use as many stops as possible in order to play very loud. However, your concern should not be how loud the prelude and fugue will sound but rather how well the polyphony will be heard. Remember, that even on a 3 or 4 manual instrument you don‘t necessarilly have to use all the stops and couplers. Often, a pure principal chorus without the couplers plus a Posaune 16‘ in the pedals (even without a mixture) will sound just fine.
If you want more thorough and comprehensive treatment of this topic with citations from contemporary sources, I highly recommend The Registration of Baroque Organ Music by Barbara Owen.
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.
Or if you want to learn to improvise in the style of Bach? If so, I suggest you check out my 9 day mini course in Keyboard Prelude Improvisation.