Q: Is this the transmission or something else - 2001 Honda Civic

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The car overheats and has problem shifting gears. When I drive, the car moves slow like it is being pulled by someone. The car has a winding sound.

Hello. Check coolant levels for the engine and the transmission fluid level (assuming automatic here - although not specified). If your Honda has the continuously variable transmission (CVT), there are a number of Technical Service Bulletins (230390 and 231604 for starters), and more importantly a Customer Satisfaction program (think "Recall" without the NHTSA involved), for failures of the CVT transmission that results in poor acceleration and strange noises as you note.

Check with your Honda dealer for these issues - this may be a "no cost" repair. The overheating problem is probably unrelated to the transmission, and should be diagnosed independently. Again, this could be related the coolant levels. Have a professional diagnose the overheating issue to have that taken care of as well

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