Depending on track rules, I cut out as much as I think is necessary (or allowable). If you race, and your track strictly adheres to ROAR regulations, then you can only have 2 inches in diameter cut from the front windshield. Usually, since it doesn't matter here, I cut out a squarish section that allows air to flow over all or most the engine head and access to the fuel tank and lowspeed needle with my long engine tuning screwdriver. My latest body has a hole that is 2.3 inches high by about 2 inches wide. For the rear window, make sure you have at least as much cut out as the front. More if you like. The side window allows a little bit of air in, but I don't feel it as totally necessary unless it allows you access to something like your fuel tank.
Make the stinger hole large enough that you wont need fuel tubing to protect the stinger from being cut. And make sure you have holes for the high speed needle, glow plug ignitor, antenna and low speed needle. Try keep all the holes as small as possible, and keep the corners smooth and rounded. The rounded edges prevents cracks and small holes keeps your ride functional but still mostly intact.