I believe Dusty understand there's only one woofer in each cabinet. If the two woofers are out-of-phase with each other the signals will cancel. To verify, place the two speakers face to face with each other a couple of feet apart. With your head in the middle listen to music with bass and note the bass level. Reverse the connections on one speaker to see if the bass increases. If it does the woofers are out of phase. Once you've determined they're out of phase, you'll need to determine where your wiring is different, internal or external. Since you've modified the speakers, I wouldn't be surprised if something was backward.

Items two and three on your list are also possible. Box volume is important to low frequency response. The larger the box the lower it can go. Also if the Xover was designed for a certain speaker with a specific voice coil resistance and inductance, it could effect impedance, thus affecting output.