You mentioned that you have a fan to pull air from upper to the lower. Is that recycled air? I think that fan may be unnecessary. If you have exhaust on top, and intake on the bottom of both chambers, then you should not need to recycle that air. It may work best for you to remove that fan and try to get the air from both the lower and upper chambers circulating towards the very top of the total cabinet, where it can be exhausted.