I can think of a couple of things to try. First, you might lower the 990's crossover point to 100Hz. (You could even back off to 80Hz, which is where Dr. Hsu apparently had it when he first demo'ed the MBM-12.) I'd also make sure to enable the VTF-3's crossover and dial it down to around 50Hz or so (the point where the MBM withdraws from the mix) so that you aren't getting both subs working in the same range.

You might consider experimenting with the phase on both subs. Assuming they aren't both in the exact same position, you may want to try both phase switches at 180 degrees and the two at different settings. One of those four possible settings (both at 0, both at 180, MBM at 0 and VTF at 180, and MBM at 180 and VTF at 0) may yield a cleaner output.

There's no reason that I can see to change your cabling - if the MBM-12 had some crossover network that took the incoming signal and divided it up, that would be a different story, but from what I can see in the manual that is not the case.