Thank you all for the advice. The fugue was giving me a devil of a time until I simplified the ostinato. Hopefully it's not too random sounding? The key modulations may be a tad bit sloppy, as well as other parts of it (though it sounds much better than the many parts I discarded... writing this thing was much harder than the passacaglia by far!). Although I'm sick of working on this, after taking a break from it for a time I may try to get back in and reorganize it more efficiently like I did with the passacaglia (as compared to its older versions).
This pieces does sound suggestive of singing (its why it made me think of a dead/drowning ships crew singing of their sorrows and adventures).
I had to take the advice I received on simplifying the ostinato to be more suitable for a fugue (but only for the fugue). Something about it is still sloppy. I can't believe how long this is now (about 8 minutes 20 seconds or so).
I saved the sibelius file in version 4 compatibility.
As for the soundfont I am using, it's called Orgue and you can obtain it here:
Organ Soundonts in a rar archive
Orgue only goes down to C3. I had to cheat by warping its sound down one octave to achieve a better range (using two channels, one deepened, one normal).
Edit: blech after giving this another listen, I'm wondering how the devil I missed all the mistakes in alignment before the romp in major keys. Well at least it's useful for ideas... and a coda. Yeah, I need to sleep.
And finally the mp3 for those who want it.
Passacaglia_&_Fugal_Inv_No1_in_Bm