If the engine's running too hot, you need to make sure the fuel you're using has enough oil, doesn't have too much nitro, the exhaust system's not too restrictive, the tuned exhaust system's properly-tuned, it's getting enough air cooling, and so on. Everything needs to be checked.

As far as the manifold bolts are concerned, you have to tighten them when the engine's cold...at room temperature. If the engine's warm, they'll never stay tight. Also, you have to use a high-temperature thread-locking compound. Regular compound will loosen with heat. You can get the high-temperature thread-locking compound through automotive parts/accessory retailers.