Bauer505

So I just got some work done to my 02 GT. I had a Exedy Stage 2 Clutch put in and got the flywheel resurfaced, I also had ford racing throwout and pilot bearings put in. While he was under there he flushed my trans fluid and put some new fluid in. My old clutch was falling apart and needed to be replaced. I got the work done by a local mechanic whom I trust does a great job. After the job I do have some conerns though, some of which I dont think even have to do with the clutch job. There was a noise that originally I though was due to my bad clutch but the noise has persisted since the work. When I am sitting at a stop in neutral and I let the clutch pedal go I can hear a whirring/grinding noise, not really bad grinding but you can hear something spinning down there. After some research I am starting to think this is the input shaft bearing. Does this sound correct to everyone? Also, my clutch pedal has started to stiffen up as ive heard is the norm for a new clutch as it is broken in, which is good because it started out pretty light. But the pedal is also starting to feel a little weird, almost like the cable has gunk on it or something, or is dragging when I press it in and release it. And today the car has started to shake when moving from a stop, not really bad but just enough to notice. What are you guys thinking I should do in this situation? I definitely need to take the transmission in to get looked at I know that. But any other suggestions? Thanks for any help.