It is obviously not the alternator, as he still has a .8 volt drop from battery to amp, and that is just way too much loss.
Either the batteries are not cabable of discharging fast enough to feed the amplifier, or you need to runs from the batteries to the amp. (which is possible, you just have to "y" the two runs together right before the input to the amp) It should not be viewed as a bottle-neck, becuase resistance of wire is a function of length. If there is only a 2" single thickness of 1/0, and the rest of the length is double, the voltage drop at the amp would be reduced. Furthermore, those dekas have relatively high internal resistance, and their discharge rate isn't fabulous, being as they were designed to be deep cylce. (low amp discharge across a long period of time, rather than a high amp discharge accross a short period) A higher quality audio battery, or a starting battery can physically supply short duration burts of amperage much better than a deep cycle design.
BTW, .5 volt improvement at full tilt is not a waste of money. Supposing that the amp draws 400 amps at full boogie, (which is what that amp should draw at .5ohm) equates to 200 watts better at the subs, plus being higher in the efficiency curve of the amplifier will increase output even more. The stock unit does 65 amps at idle, the Mechman unit does over 150 at idle. That is two and a half times the output, plus the larger case will deal with the heat/load much better that the smaller case stock unit.
Get the current flow problem resolved between the batts and the amp, and you will see even more improvement from adding the HO alternator.