problems with my system

Hello everyone...  So, I just wired up my new system in my 350Z, and I'm having issues.  At this point, after all the troubleshooting, I can't figure it out. 

The system is as follows:  Headunit is a Pioneer AVIC-Z2 (upgraded to Z3 firmware), capacitor is a Tsunami X15HCAP-40 (40 farad), the sub is an Alpine SWX-1243D (Type X, 12"), and the amp is an Alpine MRD-M1005 (digital D, mono, 1000w continuous).  The sub is in custom built fiberglass enclosure, with roughly 1.1 cubes.

So here is the problem:  I'm getting very low output from it.  I've tried all the settings on the AVIC, I've tried adjusting the amp.  Tested the cap.  Tried two different grounds.  Nothing is helping.  To get even slightly decent output, I have to set the gain all the way to 0.1.  I'm getting a lot of clipping from the sub too, and it seems to be running hot.  Not terribly so, but hotter than normal I think.  The other thing I've noticed, is that at lower volumes (about 8-10 on the headunit) I'm getting deep, low bass at a somewhat acceptable sound level.  But if I turn up the volume, the sub starts to get quieter, to the point of no bass coming from it at all.  And here's the really strange thing...  The sub is still moving!  It seems to be hitting full excursion, but there is nothing coming out of it.  When I turn the volume back down, I start to hear bass again.  I've tried reversing phase, but that didn't do it either.

So yeah, I'm just really lost, frustrated, and sad.  If anyone has advice, or can help, I would really, really appreciate it.  Thank you all in advance!

Oh, I forgot to mention how everything is wired...  The sub has dual 4 ohm coils, and I have it wired for 2 ohms at the amp, using the jumpers included with the sub.  Wire is connected to voice coil 2, as in the diagram that came with the sub.

Thanks for the advice guys. 

I just checked the wiring, everything looks right.  Ohm load is correct at the sub and at the amp.  The wire connections and the VC bridge on the sub itself are right also.  So I don't think its out of phase.

Anyone have any more suggestions?