Well, first things first - it's certainly an interesting looking fighter, although a tad hard to see through all the black lines. The big wheel is certainly interesting, design wise - is that supposed to be the cockpit, or some kind of sensor apparatus? If it's the former, I'd say maybe consider adjusting the shape a bit so that it looks a bit more like it was built around the pilot, rather than the pilot slotting into a predetermined shape. But that's just me there - I guess I can see how changing that part would mean adjusting the look of the ship a bit too much.
I like the underslung weapon pods on the wings - reminds me a lot of Steve-O's federal fighters (BP used them for the UEF). The wings themselves, though, could probably do with a few more polies - at the moment they look like they'e been asymmetrically triangulated as well, I'd probably want to fix that.
As for the technical stuff your hierarchy and whatnot - most of that could probably be done much more easily in PCS 2, after you've converted it to Pof. I suppose they could be done in Blender, technically, but you're far less likely to have problems (naming inaccuracies and whatnot) if you do them with PCS, and IMO it's just an overall simpler process. But each to their own.
