I am writing an essay about the synthesis of music theory Bach used to create his own music theory, especially in his fugal works. Any help would be appreciated, but if people could provide sources and books I could use, that would be greatly appreciated.
I would rely on Christoph Wolff's excellent Johann Sebastian Bach. The Learned Musician (published 2001), which features an entire chapter about Bach's great interest for previous and contemporary composers, and also his Bach: Essays on his Life and Works.
You should probably focus on the German "fathers" of Bach's keyboard style (other Bachs, Pachelbel indirectly, Böhm and Reinken, but most importantly Buxtehude, whom he personally met, and Händel and Kuhnau later on) — but it would be an oversimplification to exclude that the French organists and the Italian masters might have had some influence on his contrapunctal technique. We know for a fact that he owned and analyzed copies of Grigny's five-parts organ works and Frescobaldi's Fiori. Not to mention the theoretical treatises of Zarlino, Gaffurio and others. (see sources above)
We can clearly see an evolution in his choral, orchestral and instrumental styles from his Mühlhausen years to the later Leipzig period; the best example of this is, prominently, the two volumes of the WTC — the first written between Weimar and Cöthen, the latter completed in the first 1740s. An experienced musician can almost immediately point out which Theil a prelude or a fugue belongs to just by listening to it.
Bach was like a sponge, constantly assimilating new techniques and stimuli from the musical world around him, with a special devotion that led him to thoroughly master most of the genres of his time — all of this without ever traveling outside of northern Germany. He felt that a good musician should be an informed musician: in a time where collecting manuscripts and editions from all around Europe (with no internet!) was a costly task, this is an impressively modern and mature point of view. A not much cheaper alternative would have been going to study in France or Italy, as many of his colleagues did (Händel, Heinichen and Pisendel foremost).
Hope this can still help
You might try "The Bach Reader," which is a compilation of contemporary articles and letters. http://www.amazon.com/The-New-Bach-Reader-Sebastian/dp/0393319563
There are a bunch of biographies (Too many to list) Forkel's and Schweizer's are notable but not very modern.
The J. S. Bach wiki notes that Bach's older brother, John Christoph, had been a student of Pachelbel (canon) and that Bach spent two years in a music school in Luneburg studying with George Bohm.
The subject of your essay is especially difficult because Bach was not an innovator. In addition, music theory at that time was not as clear and usable as it is today. Theoretical books about counterpoint, such as Fux's Gradus ad Parnassum (1725), were aiming at Palestrina's style, not at the contemporary style. Harmony theory was still in its infancy; Rameau's treatise, although one of the best for the time, includes a number of oddities.
So Bach style probably owes more to his tremendous work of studying and copying other composers scores, than to theory studies.
However, in his late fugal writing he definitely liked elaborate relationships between phrases that are mainly apparent when reading but not when hearing (inversion, retrograde...). This was not new in music history, but was more developed during the 16th century than during the 17th and 18th centuries. Music history is a perpetual oscillation between complexity and simplicity, at least when each component of music (melody, harmony, counterpoint, rythm...) is considered separately, and Bach's time was leaning towards counterpoint simplicity. Bach gave a last fight for a cause that was already abandonned.