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Don't think it has anything to do with the brakes, unless its the vacuum check valve. The brakes pedal gets hard like there is no vacuum booster. I replaced the booster about six months ago but not the check valve. If the egr valve gets stuck open couldn't that cause this to happen, by making the computer think the car is running lean and flooding the engine with fuel which would make the CAT start to heat up? It doesn't happen often and the brakes don't get un-normally hot.
The pedal does come up to the top with no slack, almost like it is being pushed up. I have not checked the CAT with a temp gun. I will do more checking and get back to you but I will not be able to work on the car again until Monday.
I have talked to some other mechanics about this issue. I have been told that the flex hoses to the front calipers are known to fail inside, creating flaps which act like a check valve. I have tried to get the car to "act up again" but it is behaving normally. I have replaced both front flex hoses and the master cylinder and hope this issue does not return. Thank you for your help in solving my problem.