Hyundai Santa Fe Gearbox & Transmission Problems

ABSOLUTELY yes. Take it up with Hyundai directly. It seems you have been given the run-around by the dealer and the company needs to know. The clutch would probably need to be replaced when the flywheel was changed as they are most likely to be different, but Hyundai should cop the cost. It sounds like a design problem. And it could be a cause of your belt failures and your ignition problems.

MOST vehicles have a diff whine, it's the nature of the type of gears used in diffs, but you rarely hear it. Most car makers manage to isolate the noise so it doesn't travel through the car. They use all sorts of techniques to ensure it doesn't become a problem. The problem with the Santa Fe could lie in the diff itself, it could also lie in the suspension or body which can act as amplifiers. I would take up Hyundai's offer and have them fix the problem.