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Q: Bad Brake Booster or Vaccum Loss or Something else? on 2000 Ford Contour

Engine light is on.
Tapping the gas pedal while the engine is running and in park causes a clicking noise from parking break / transmission area, car is very hard to break until in gear and then it clears up.
Also, related or unrelated, there seems to be some irregular acceleration lag once under way.
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Get the check engine light diagnosed ASAP. The check engine light indicates that the computer has detected a malfunction in the engine/emission control system and has diagnostic codes and data stored which would be essential in diagnosing the problem.
You may have a vacuum leak affecting the power brake system which will affect the way the engine runs.
Find a Ford expert and get it diagnosed.
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