I have the same problem on my 3700BQE.
But I wonder if raising the HDs won't obstruct the airflow.
When the Hard disks (I have three) are placed normally
you have holes in between them to get the airflow to the
back of the case. But raising the HDs, wouldn't it obstruct the air?
I am thinking of removing the HD case and placing the HDs in
the upper bay with something I don't now yet.
Maybe the zalman HD system or the Sunbeam HDD silencers.
But in the upper tray the HDs have no airflow at all..
I will search a bit more on this forum, but your idea is a good one.