Hi Heather,
NIce project. The bass issue (lack of bass) when you moved the cabinets to the top of the audio/video rack from the floor, is the result of:
The rack itself. The low frequencies are absorbed in the wood. The window behind the speaker cabinets is also a factor. The bass energy is also absorbed there.
The best location is on the floor next to 2 walls. I have my 4507 cabinets as follows:
The left side is next to a sliding door and a solid wall behind. There is a great deal of low frequency loss due to the sliding door. The low frequency energy is used to move the doors.
The right side is located at a 90 degree point. 2 solid walls. Bass response is extended. Both speakers are on the floor.

Try moving the cabinets where you first had them and listen for a while.

Ron