Have a 2004 focus 2.3l, had similar problems, poor performance, loud like muffler bad, clucked when you firs started it, rough idle in gear but fine when in park, poor mileage, etc. Tried everything; new throttle body, throttle body speed motor, PCV valve, intake cleaning 1500 bucks later got the mileage back but the cluck on start rough idle while in gear, noise, and hesitation were still there. Replaced motor mounts and WOW new car. Second guessing all the other items I did. Ford guy said focus has issues with motor mounts.
Hope this helps you save the pain I went through.
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Wednesday, March 12th, 2014 AT 6:11 PM