Grinding Noise

I have a 2000 GT 5spd. Yesterday i installed a short throw shifter. Today when i started my car i noticed a grinding noise, sounds like it is coming from underneath the shifter. I never heard this noise until today. I also noticed that it goes away when i push the clutch pedal in, and it gets louder as my engine revs. Doesn't matter if i am in neutral or driving in gear i still hear it and it gets louder as the RPM goes up. Any ideas would be greatly appreciated. Thanks in advance.

I'm hoping its just normal noise that i may not of heard with the stock shifter installed. And i did leave the plastic boot in when i removed the stock and installed the new. When i had the cable, quadrant and firewall adjuster installed the shop said that from what they could see through where the inspection plate was removed everything looked good and the clutch felt like it was ok when shifting and stuff.