Four problems related to clutch pedal/linkage have been reported for the 2006 Honda Civic. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2006 Honda Civic based on all problems reported for the 2006 Civic.
The drive-by-wire throttle system equipped on the vehicle has been very tardy in its response time to throttle-pedal input. This was already a "recall" for this vehicle, and has since gotten worse after the new software was installed on the vehicle. For instance, if downshifting into first gear, quite often will the engine accelerate itself and push the vehicle for extended amounts of time (10-15 seconds) with no pedal input. This has occurred not only in first gear, but also fourth gear and sixth gear, not while downshifting but during normal highway driving conditions. The total number of incidences of this is approximately 10. Luckily I do have a clutch and when depressing the clutch, the engine will raise its revs from ~2000 to over 3000 and then drop off to idle. As well, while shifting gears, throttle response time from pressing the accelerator pedal is slow, and when releasing the throttle pedal there is a 1. 5-2 second delay. Not so safe in heavy traffic.
My 2006 Honda Civic si has an issue with "hanging revs" that even after the release of the gas pedal the rpms seems to stay steady for 1-2 seconds. The inability of the dbw system will eventually lead to early clutch failure, also there is surging and jerking in 1st-2nd gear. I must say that it makes me very nervous to drive because I can't predict what the car will do. The car also seems to have a notchy, stiff, and grinding 3rd gear that won't seem to go away even with recommended fluid.
(a) notchy shifting (b) resistance going into 3rd gear (c) grinding related to 3rd gear (e) transmission kicking out/popping out into neutral from 3rd.
The vehicle has a manual gearbox and the clutch pedal is very stiff to operate. This combined with a fairly long travel could require short divers to position their seat very close to the steering wheel in order to get enough leverage in their leg to fully depress the clutch pedal prior to staring the engine. The incident date is non-specific as this is an ongoing issue. I have raised my concern with the local dealer and was advised that they cannot reduce the stiffness of the clutch action or reposition the engine disconnect switch (so that the pedal does not need to be pressed to the floor).