Hello Mike,
My first suggestion would be to install all of the factory parts (parallel feed capacitor and 0.1uF interstage coupling capacitor), then let the amp burn in for 100 hours.
At that point, you can have a baseline for the performance of the amplifier.
The bass response differences may have to do with the feedback and damping of the other amplifier, but there isn't a good way to know when the amp isn't stock.
-PB