One problem related to transmission noise has been reported for the 1999 Hyundai Elantra. The most recently reported issues are listed below.
Transmission would make clunking/shattering and whinning noises. Took to dealer & transmission replaced with new one. The whinning & shattering noises still exist. Had the final drive unit (transaxle) & bearings replaced. It had a high pitch whine. After replacement, noise still exists, but now it bucks.