Hi Kyle,
Thanks for your question. My first piece of advice is for you to find an organist to help you decipher the music. Many organ works show the pedal on the same staff as the left hand and, in order to parse out which part is which, you need to be able to know how the voices work. Often the music doesn't specify pedal - but if you are playing an organ work, it's likely to be assumed you would use the pedals as well as the manuals. (Some pieces can be played on just the manuals as well, which is why it's not always broken out as a separate pedal part.) This page of the Fugue is indeed a 4-voice fugue. The voices are distributed between the two staves depending on where the melody goes. Sometimes one or more voices rest, but there are 4 in total.
If you can't find an organist to help you, I would consider finding another music transcriber to take the project who understands organ music. Or at least find someone who you could contract to highlight the pedal line.
Sorry it's not an easier and straightforward answer!!