Well, FYI, you shouldn't have to leave the sides off of your tower. It's actually not good for it (although, if the 'hot spots' are overheating, sometimes you have to). The reason is because you are supposed to be drawing air through the system, cooling everything in the path of the air flow. With the sides off, the only thing getting cooled are the things that have a heatsink and fan mounted on them (items with only a heatsink still get cooled, but much less than they would with air flowing over them, and ofc items that don't have a cooling device just sit and build heat).
Say, for example, your hard disk. Depending on your motherboard model, your northbridge could be getting hot. (Some motherboards actually have a heatsink / heatsink + fan mounted on the northbridge). Your memory also may be heating up.
Of course, in your circumstance, you have to keep the sides off until you get your problem fixed, I'm just saying, don't stop until you've got your system holding a good cool temperature with the sides on.