Thought I would post an update if anyone is interested- I decided not to do any drilling. Instead I changed the shelf spacing to give about 3 1/2 inches more space above the amp.
The rack I use isn't really designed to allow for changing shelf spacing but it wasn't too hard to do. The shelf spacing is controlled by the aluminum tubes at the corners. I ordered an aluminum tube from McMaster and cut it as needed. As long as you keep the total length the same you can change spacing however you want by replacing the stock tubes.
Anyway now it runs much cooler. The stand seems a little less rigid, probably due to the taller shelf spacing, but I am willing to live with that.
Mark