03 elantra manual tranny noise

hi, i have a elantra with 86k miles on it. The tranny started making a growl sound. When the car is sitting still with the motor running, and the clutch not pushed in i can hear it. When i push the clutch pedal the noise goes away. if i put the tranny in gear with the clutch pressed i get no noise. but when i release the clutch, the growl comes back. i was hoping it was the throwout bearings, plus i found the clutch starting to slip. So i replaced the clutch, pressure plate and throwout bearing. But the noise continues. A freind who owns a shop told me it sounded like a input shaft bearing. i cant hear the noise in 4th or 5th gear. i called the hyundai dealer, They want 220 dollars to diagnose the tranny, i was told if its a transmission issue they will waive the fee, because it will be covered by the 100k warranty. is there anything i should check before taking it in on friday?. thanks i appreciate any and all help! Jim