Been away for a while, but I thought I'd pop in and give my, I know, rather opinionated thoughts
Overall, your rendition of this P&F sounds much better prepared and more solidly executed to my ears than some of your earlier ones, especially the prelude. Good clear voicing in particular. The fugue could perhaps profit from some more practice, but, as you might say, it is one tricky bastard of a piece (IMO one of the more difficult in Book I). Some specific thoughts/suggestions:
Prelude: I rather like your relation between the fugal chorale section and the intro. It does sounds exactly in time to me. Personally, I would probably play it faster by comparison, which may be permissible given Bach's ubiquitous lack of tempo direction, but perhaps yours is the most proper way. Nice clear scale passage to end the intro, though the culminating trill sounds uneven to me. I like very much your voicing throughout. Some rather strange-sounding hesitations (to my ears, though this may be intentional, as you say), and the left hand sounds a bit flabby and unsure in just a couple of places (a few dropped, unclear notes). Overall, though, nice rhythmic pulse. Nice allargando effect to end.
Fugue: I like your opening gesture, which sounds very clear and direct. The tempo may be just a bit fast, which results in a bit of sagging later on. My principal concern, though, would be too much pedal use, which tends to make the sound sodden and unclear. Also, I'd say the trills, particularly those in the left hand on the second page, need a bit more work (I had a devil of a time with those myself).
Nice job overall, though, and keep up the good work as you venture on with your WTC re-recording project!