Subject: Manual tranny noise
Question: 96 Eclipse, 2.0L GS 5 Speed Manual.
I have a noise that sounds like a throw-out bearing going bad. I have replaced the bearing, and still the same noise. I took it to the dealer and they said it was the clutch. I have replaced the clutch and took the flex plate off and had it inspected. After it was all back together I still have the noise. It has become very loud now and you can feel it on the front of the tranny. Any sugestions?
Answer: Scott,
This sounds you may be experiencing the "walking" crankshaft syndrome. It normally affected the 2.0L turbo engines, but non-turbos may have it too.

Basically, the crank shaft would develope lateral movement. The symptoms in most the cases seemed to be problems with putting the car into gear. The transmissions were fine. The problem is faulty crankshaft bearings. The front of the motor would make noise when the clutch is engaged/disengaged... bad thrust bearing on the crank. There are lots of articles online describing the 2G DSM "walking" crankshaft problem.

If you take your car back to the dealership, have them look up the Technical Service Bulletin regarging this crankshaft issue. They'll typically have to replace all bearings and maybe even your crankshaft if it has been gouged. The crankshaft should have zero horizontal play.
Good luck!