First, make sure that it is indeed a heat issue causing the stalls. Open the case, aim a common housefan into it. Turn it on and give it a good hard run. If that happens to fix the problem, There are a few very cheap ways to improve the airflow in the PC.
One way is like onespeedreed said.... make a nice vent in the front. Several sites around about "modding" a case vent into your PC. Or you could go the route I did... watercooling.
Seriously, there are products you can buy that will place a fan right under your video card to help get some air to it, and a higher performance heatsink for your CPU wouldn't be that big a chore or kill the bank.