Ok, sounds like where we need to focus is the wiring, and possibly the crossover points.
Your explanation made complete sense, less one part--you said the subs are wired in series 3 -3.
what exactly do you mean like this?
3 subs to a series, or wired at 3 ohms mono, etc?
According to the info that I have The Thunder 8000 subs are 4 ohms each. This would mean that with an 81000D amp on each set(2) subs with series wiring, there would be a final impedence of 8ohms for each set(2) subs. If they were wired in paralel, the final impedence would be 2 ohms per set(2) of subs.
The 81000D has optimal output at 2 ohms.
Right from the MTX site--->
Specifications
Power 12.5 VDC Input
2 Ohm Load 1000 w x 1 Low Level
4 Ohm Load 500 w x 1
Crossover(s)
Power 14.4 VDC Low Pass 40Hz-200Hz -
2 Ohm Load 1500 w x 1 Variable
4 Ohm Load 850 w x1 RCA Output
Low Pass Only
Dimensions
(with ISO Feet) Other Features
Compression Circuitry
17.8" x 9.75" x 2.1" Thunder EQ
45.2cm x 24.8cm x 5.3cm EBC2 Port
http://www.mtx.com/caraudio/products/amplifiers/thunder81000d.cfm
I would suggest re working the wiring so that each set(2) of subs is at 2 ohms. This should fully utilize the complete potential of the amp.
Take it easy,
-zane