Problem solved!
In my effort to make the storage area of the box as large as possible I condensed the size of the Hideaway compartment. I gave it adequate space for ventilation but failed to realize the 3.5mm input plug for the remote bass gain controller needed more space.
After my make over on the controller mount I plugged it back in the Hideaway and tested again. It worked fine till I snugged the woofer in place. The rumble came back once again. I realized it was in a bind and was bent.
I did some research and discovered the solution to my issue. They offer a 90 degree mini rca connector or an adaptor. I opted for a pigtail and replaced the connector entirely.
This proved to be a good choice. The original connector was now damaged, so the new one resolved multiple problems.