Sorry about the wiring - You ordered two π kits rather than tower two π's, and the cable assemblies included in the standard bookshelf version kits are shorter. There is no difference in the components in the two kits, but there is a little difference in the wiring harness and the ports. The bookshelf version has shorter wires so that there isn't a bunch of wire in the cabinet just looped around inside. The towers need 5 foot length, so the cable assembly is longer. I also include a strain relief in the tower kits since longer wires will be supported. But the tower kits do not include port material since none is needed, and the bookshelf version includes a duct.

About the bass, double check everything - The wiring, phasing, connection to the amp, etc. I've never heard anyone comment that the towers lacked bass; The comments are always quite the opposite. So I think there may be something wrong, and more than could be explained by break-in. I suspect phase might be the culprit, so reverse the wires on one speaker and see if the bass is increased. If that's the problem, you'll notice a significant difference after reversing the wires.