Dear Vincent,
Had a chance to listen shortly to your sound file.
First I really want to tell you that it's a very good thing that you're working on historical styles, because that's such an important "tool" and "handcraft" for any serious and professional contemporary composer, in my opinion.
Maybe you can post an extract of the written score, so it would be easier to comment, if you really want seriously to improve that technique and to be commented on details, etc.
I think that's what you're looking for, so I gladly comment honestly because my ears for counterpunctual writting are quite sensitive and maybe I can help you a little, of course only if you really wish.
It's a nice fuga subject that you've created, Vincent. You're in c#-minor as far as I heard by listening to it only once but ended in B-major, that's quite unusual, although I know it's probarbly not the real ending of the piece (I will talk about it later on...)
As soon as the second voice ("Comes") enters there're some issues about the dissonances. You're theme starts with the famous fifth (C# - G#) and you answer it with g# and c# that is correct because it should be better answered "tonal" instead of "real" (or "absolute", sorry, I don't know the correct english terms) but then you have B (in the upper voice) and down "A#", try intead of B "B#" (it's the major third of G#-major, the dominant of your tonic c#-minor) then the "passing note" or "changing note" that you have and it's dissonance will be correct.
At the same passage, if I heard correctly, you have in the first voice (that has become now the "counterpoint" as soon as the second voice entered with the Comes) melodically an audible "triton" (I think the voice goes down from "E" to "A#"), such a thing Bach would have tried to avoid or "hidden" as much as possible (that's a kind of art in counterpoint).
If you could post the score I could mark you the passages that I mean and give you possible solutions, in order to come closer to the Bach-style that you're apparently trying to archive in this piece.
At the end of the sequence you have a dominant7/13 chord. That way as you wrote it would not be written in "baroque style" it comes much, much later in the romantic periode.
I know that Bach has many kind of "crazy" chords already in his wonderful music, but those kind of chords appear in a different way, for example by the use of "passing-dissonances", or especially as a "grace" ("Vorhalt", german) example in all his wonderful Chorals you can find that stuff, but they always dissolve in something else, because they are just "grace notes".
Then you end the sequence on "B" that is quite unusual and very far (well actually, just theoretical it can bee seen as the Dominant of the tonic-parallel), I'm asking myself how you're planing to continue because on this cadence usually you would bring again the theme.
Usually in the style of Bach it would be possible if you bring now for example the Themes again in it's:
.) dominant key (in your case "G# major)
.) parallel major key (E-major)
.etc.
Just some little things I heard by listening to it just once. I hope I didn't scare you too much, but I thought as you wrote you'd like to improve and want comments, I just write what I hear.
If you're really seriously interested in this wonderful "chapter" im music (fugas, counterpoint, etc.) maybe you're working on that at the moment, than I'm really glad if I can give you some advices, just feel free to write me a mail or something, you can also send or scan me your scores and I can comment them if you want. It's always easier to comment music that I can read.
Hope it might have been a little help
Keep on writting and best wishes!