Originally Posted by QcCowboy

there are a lot of harmony issues (like when the 3rd voice comes in).
the score, unfortunately, is a bit annoying to read. is there any way you could post a MIDI instead? or better yet, a PDF?

In the first staff, near the last measure, if I recall, I noticed some parallel 5ths. They were "disguised" and COULD, if one wanted to be very liberal, be dismissed, but I did hear them, and generally, parallel 5ths properly disguised should not be audible (there are actually numerous examples in Bach's music of disguised parallel 5ths... the audible result however is that you don't hear the 5ths at all).

There are more egregious errors, like at the entrance of teh 3rd voice, where not only is the harmony not clearly identifiable, but there are parallel 8ves with the alto.
At the 4th voice entrance, the harmony is too indestinct, and then promptly resolves to a 2nd inversion (including some more parallel octaves between alto and bass).

I think you have a bit of work to do in counterpoint before attacking something as ambitious as a fugue. But trust me, the work WILL pay off in the end. I think counterpoint is the one course I regret the least of all my years of musical study. Even in music that is not strictly "tonal", it still has principles that apply and help keep cohesiveness.