V6 Tranny Noises
 

I've got a 2000 V6 Mustang and I just installed a Pro 5.0 shifter in it, and shortly thereafter the transmission (i believe) started making a whining noise in 5th gear. It seems to be noisier all around, but 5th gear has a loud whine that is really annoying if the radio isnt on. What might be causing this?

Also, my clutch pedal sometimes vibrates back and forth and rattles, what can I do to fix this or what does it mean??

Thanks!