[xlr8or]

If you are sure it's a heat soak problem get the car warm so it starts acting up and put an ice pack on the coil and msd box to see if resolves it. If it does you know where the problem is.
You might also want to check your fuel line. Make sure it's not too close to the exhaust and causing a vapor lock. The fact that it runs but stumbles may be the fuel isn't getting to the carb when hot and letting it sit get the fuel bowls full again.