I've been doing this for over a year now with no heat problems. I'm in the same boat as you with the handles being in the way. Lot's of amp head/rack cases don't have much in the way of ventilation through the top, but some do have a bit and some also have fans. I say go for it as is and if you get worried, turn on an overhead fan or set one up at least a good distance from the setup. Wouldn't want that motor's magnetic field giving you issues. You could also buy some really big feet for the rack or cut some scr@ps of wood and paint them black to go between the head and the rack.